Upgrade from 2.4.8 to 3.1.1.0

Our Journal site is www.threatenedtaxa.org and the version we are using is 2.4.8. We tried to upgrade from 2.4.8 to 3.1.1.0 and facing quite a lot of problem.

I keep getting the following message. Earlier also this happened and you had told me to clear the corrupted database and import freshly. I have been doing that but getting the same error message.

A database error has occurred: Duplicate entry ‘fontsizeblockplugin-0-context’ for key ‘plugin_settings_pkey’

Hi @latha_ojs,

Using the command-line based upgrade process, can you post the output you get when you run the upgrade?

Regards,
Alec Smecher
Public Knowledge Project Team

Here is what I get

threatenedtaxa@threatenedtaxa.org [~]# php /home/threatenedtaxa/public_html/tools/upgrade.php upgrade

PHP Deprecated: Comments starting with ‘#’ are deprecated in /usr/local/lib/php.ini on line 550 in Unknown on line 0

[pre-install]

[load: upgrade.xml]

[version: 3.1.0.1]

[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]

ERROR: Upgrade failed: DB: Duplicate entry ‘fontsizeblockplugin-0-context’ for key ‘plugin_settings_pkey’

please help me how to go about this.

Please let us know how to solve this issue

Hi @latha_ojs,

I think you have some bad data in your OJS 2.x installation. What do you get when you run the following SQL query on your 2.4.8 database?

 SELECT * FROM plugin_settings WHERE LOWER(plugin_name)='fontsizeblockplugin';

Regards,
Alec Smecher
Public Knowledge Project Team

Here is what I get. Do I have to remove the doubles? I am not expert in PHP but can do if you advice me. Thanks and regards Latha

Hi @latha_ojs,

I’m afraid that image is too blurry to read – can you post it another way?

Regards,
Alec Smecher
Public Knowledge Project Team

I am really sorry!. Here is the good resolution file.

Hi @latha_ojs,

Hmm, that looks fine. Can you run the upgrade process again, and run the same query after the upgrade has failed?

Regards,
Alec Smecher
Public Knowledge Project Team

Hi,

I run the upgrade again as you asked. The upgrade stopped with the following error:

packet_write_wait: Connection to 185.80.220.33 port 8788: Broken pipe

I am not an php expert but will do if you tell me how to go about it. Thanks in advance, Latha

Last login: Tue May 8 18:22:15 on ttys000

lathadevi:~ lathadevi$ ssh -p 8788 threatenedtaxa@185.80.220.33

threatenedtaxa@185.80.220.33’s password:

Last login: Sat Apr 21 10:55:37 2018 from 103.81.34.196

perl: warning: Setting locale failed.

perl: warning: Please check that your locale settings:

LANGUAGE = (unset),

LC_ALL = (unset),

LC_CTYPE = "UTF-8",

LANG = (unset)

are supported and installed on your system.

perl: warning: Falling back to the standard locale (“C”).

perl: warning: Setting locale failed.

perl: warning: Please check that your locale settings:

LANGUAGE = (unset),

LC_ALL = (unset),

LC_CTYPE = "UTF-8",

LANG = (unset)

are supported and installed on your system.

perl: warning: Falling back to the standard locale (“C”).

perl: warning: Setting locale failed.

perl: warning: Please check that your locale settings:

LANGUAGE = (unset),

LC_ALL = (unset),

LC_CTYPE = "UTF-8",

LANG = (unset)

are supported and installed on your system.

perl: warning: Falling back to the standard locale (“C”).

perl: warning: Setting locale failed.

perl: warning: Please check that your locale settings:

LANGUAGE = (unset),

LC_ALL = (unset),

LC_CTYPE = "UTF-8",

LANG = (unset)

are supported and installed on your system.

perl: warning: Falling back to the standard locale (“C”).

perl: warning: Setting locale failed.

perl: warning: Please check that your locale settings:

LANGUAGE = (unset),

LC_ALL = (unset),

LC_CTYPE = "UTF-8",

LANG = (unset)

are supported and installed on your system.

perl: warning: Falling back to the standard locale (“C”).

threatenedtaxa@threatenedtaxa.org [~]# php /home/threatenedtaxa/public_html/tools/upgrade.php upgrade

[pre-install]

[load: upgrade.xml]

[version: 3.1.0.1]

[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]

packet_write_wait: Connection to 185.80.220.33 port 8788: Broken pipe

Hi @latha_ojs,

It looks like the upgrade was running OK, but your SSH connection was closed (probably due to inactivity), interrupting it before it could finish. This is more of a network/command line question than an OJS question, but you should be able to use a built-in tool like nohup to allow it to finish. Note that you’ll have to restore your database and files area from backup before running the upgrade again.

Regards,
Alec Smecher
Public Knowledge Project Team

Hi,

I am getting the same error again and again.

Could you please tell me whether it is possible to upgrade the files in my computer and upload everything back. If yes, please let me know the instructions to do the same.

Sorry for the trouble,

Thanks and regards

Latha G. Ravikumar

Hi @latha_ojs,

This is my 2 cent. I previously did local upgrade and upload all back to the live site via FTP.
This method is used to get around the connection time limit in SSH or sessions time out in live web upgrade process.

  1. Use XAMPP to create web environment in your local computer.

  2. After that, follow the usual full upgrade process from PKP.

  3. Using the OJS 3 files, recreate your site within XAMPP. (Copy your public/ folder, files_dir and import your database. Configure it using the new config.TEMPLATE.inc.php.).

  4. Upgrade, either via web or command line

  5. If successful. Put them all back to your live site via FTP

ps. Please, don’t use OJS 2 program files and overwrite it with OJS 3. The residual files will cause you trouble later.

Hope this helps.

Hi,

I am trying to do test upgrade via localhost. After upgrading, html galley images are not showing. Html gally opens but the images seems missing.

Please let me know what to do.

thanks and regards

Latha

Hi @latha_ojs,

We’re about to release OJS 3.1.1-1 later today, and it has a few tweaks to the upgrade process. I’d suggest waiting for that release, trying your upgrade again, and seeing whether that resolves the issue.

Regards,
Alec Smecher
Public Knowledge Project Team

Thank you. Will wait for the new release.

Hi Alec,

I tried upgrading OJS 3.1.1-1. I got a blank page while upgrading and after that I could not resume the connection.

I checked the log error and find the below errors.

[Wed Jun 06 17:01:09.656460 2018] [ssl:warn] [pid 892] AH01906: www.example.com:443:0 server certificate is a CA certificate (BasicConstraints: CA == TRUE !?)

[Wed Jun 06 17:01:09.656714 2018] [ssl:warn] [pid 892] AH01909: www.example.com:443:0 server certificate does NOT include an ID which matches the server name

[Wed Jun 06 17:01:09.815955 2018] [ssl:warn] [pid 893] AH01906: www.example.com:443:0 server certificate is a CA certificate (BasicConstraints: CA == TRUE !?)

[Wed Jun 06 17:01:09.815985 2018] [ssl:warn] [pid 893] AH01909: www.example.com:443:0 server certificate does NOT include an ID which matches the server name

[Wed Jun 06 17:01:09.827011 2018] [lbmethod_heartbeat:notice] [pid 893] AH02282: No slotmem from mod_heartmonitor

[Wed Jun 06 17:01:09.993971 2018] [mpm_prefork:notice] [pid 893] AH00163: Apache/2.4.33 (Unix) OpenSSL/1.0.2o PHP/5.6.36 mod_perl/2.0.8-dev Perl/v5.16.3 configured – resuming normal operations

[Wed Jun 06 17:01:09.994027 2018] [core:notice] [pid 893] AH00094: Command line: '/Applications/XAMPP/xamppfiles/bin/httpd -E /Applications/XAMPP/xamppfiles/logs/error_log -D SSL -D PHP’

thanks and regards

Latha G. Ravikumar

Hi @latha_ojs,

That log looks like it might be your Apache log, not your PHP log; sometimes they are different files, depending on your server configuration.

Regards,
Alec Smecher
Public Knowledge Project Team

Today I tried via command prompt but don’t know whether the installation is over.

threatenedtaxa@threatenedtaxa.org [~]# php /home/threatenedtaxa/public_html/tools/upgrade.php upgrade

[pre-install]

[load: upgrade.xml]

[version: 3.1.1.1]

[code: Installer Installer::checkPhpVersion]

[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]

[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]

[data: dbscripts/xml/upgrade/3.1.1_preupdate_citations.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::installDefaultNavigationMenus]

[code: Installer Installer::migrateStaticPagesToNavigationMenuItems]

[code: Installer Installer::migrateSRLocale]

[code: Installer Installer::concatenateIntoAbout]

[code: Installer Installer::concatenateIntoMasthead]

[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::provideSupplementaryFilesForReview]

threatenedtaxa@threatenedtaxa.org [~]#