Upgrade from 2.4.8 to 3.1.1.0


#5

Please let us know how to solve this issue


#6

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


#7

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


#8

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


#9

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


#10

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


#11

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


#12

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


#13

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


#14

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.


#15

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


#16

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


#17

Thank you. Will wait for the new release.


#18

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


#19

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


#20

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 [~]#


#21

Hi @latha_ojs,

I’d suggest checking your PHP error log to see if something is recorded there. I don’t see the “upgrade succeeded” message, so the upgrade probably isn’t complete.

Regards,
Alec Smecher
Public Knowledge Project Team


#22

Hi,

Here is the php error log. I can able to view the files but html galley image isn’t working. Also the version still says 2.4.8.

Thanks for all your help

with regards

Latha


#23

Hi @latha_ojs,

The log didn’t come through with your response – I believe the forum we use strips attachments.

Regards,
Alec Smecher
Public Knowledge Project Team


#24

Sorry!. I couldn’t send the attachment. Here is the error where the process got stuck.

[15-Jun-2018 06:28:31 America/Chicago] PHP Fatal error: Call to a member function getFileId() on null in /home/threatenedtaxa/public_html/lib/pkp/classes/submission/PKPSubmissionFileDAO.inc.php on line 1029