Anders
February 21, 2019, 8:21am
1
Hi,
I have problem upgrading OJS. When I run:
php tools/upgrade.php upgrade
root@vm-test02:/var/www/html/ojs#
root@vm-test02:/var/www/html/ojs# php tools/upgrade.php upgrade
[pre-install]
[load: upgrade.xml]
[version: 3.1.1.4]
[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]
ERROR: Upgrade failed: DB: Duplicate entry ‘anthropocene’ for key ‘submission_search_keyword_text’
root@vm-test02:/var/www/html/ojs#
The submission_search_keyword_text appear to be a new table that the script create, however there is some problem. Also it does not appear to be a dublicate key
MariaDB [ojs]>
MariaDB [ojs]> select * from submission_search_keyword_list where keyword_text like ‘%anthropocene’;
±-----------±--------------+
| keyword_id | keyword_text |
±-----------±--------------+
| 243773 | �anthropocene |
| 482508 | anthropocene |
±-----------±--------------+
2 rows in set (0.00 sec)
MariaDB [ojs]>
MariaDB [ojs]> show index from submission_search_keyword_list;
±-------------------------------±-----------±---------±-------------±------------±----------±------------±---------±-------±-----±-----------±--------±-------------
-+
| Table | Non_unique | Key_name | Seq_in_index | Column_name | Collation | Cardinality | Sub_part | Packed | Null | Index_type | Comment | Index_comment
|
±-------------------------------±-----------±---------±-------------±------------±----------±------------±---------±-------±-----±-----------±--------±-------------
-+
| submission_search_keyword_list | 0 | PRIMARY | 1 | keyword_id | A | 482508 | NULL | NULL | | BTREE | |
|
±-------------------------------±-----------±---------±-------------±------------±----------±------------±---------±-------±-----±-----------±--------±-------------
-+
1 row in set (0.00 sec)
MariaDB [ojs]>
I have tried to optimize all tables before upgrade, but since this is a new table I don’t know how to solve this problem.
I am using Debian 8
Best regards
Anders
jnugent
February 21, 2019, 3:06pm
2
Hi Anders,
You can try cleaning out the search keyword tables in your 2.4 install before the upgrade. Those would be submission_search_object_keywords, submission_search_keyword_list, and submission_search_objects. If the upgrade runs successfully you can rebuild the search index with the CLI tool:
php tools/rebuildSearchIndex.php
and see how it goes. Before you do this, please make a backup if you haven’t already.
Cheers,
Jason
Anders
February 22, 2019, 7:37am
3
Hi Jason,
Thanks for the reply but I don’t see these tables in my old install
mysql> use ojs
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A
Database changed
mysql> show tables;
±--------------------------------------+
| Tables_in_ojs |
±--------------------------------------+
| access_keys |
| announcement_settings |
| announcement_type_settings |
| announcement_types |
| announcements |
| article_comments |
| article_files |
| article_galley_settings |
| article_galleys |
| article_html_galley_images |
| article_notes |
| article_search_keyword_list |
| article_search_object_keywords |
| article_search_objects |
| article_settings |
| article_supp_file_settings |
| article_supplementary_files |
| article_xml_galleys |
| articles |
| auth_sources |
| author_settings |
| authors |
| books_for_review |
| books_for_review_authors |
| books_for_review_settings |
| captchas |
| citation_settings |
| citations |
| comments |
| completed_payments |
| controlled_vocab_entries |
| controlled_vocab_entry_settings |
| controlled_vocabs |
| custom_issue_orders |
| custom_section_orders |
| data_object_tombstone_oai_set_objects |
| data_object_tombstone_settings |
| data_object_tombstones |
| dataverse_files |
| dataverse_studies |
| edit_assignments |
| edit_decisions |
| email_log |
| email_log_users |
| email_templates |
| email_templates_data |
| email_templates_default |
| email_templates_default_data |
| event_log |
| event_log_settings |
| external_feed_settings |
| external_feeds |
| filter_groups |
| filter_settings |
| filters |
| gifts |
| group_memberships |
| group_settings |
| groups |
| institutional_subscription_ip |
| institutional_subscriptions |
| issue_files |
| issue_galley_settings |
| issue_galleys |
| issue_settings |
| issues |
| journal_settings |
| journals |
| metadata_description_settings |
| metadata_descriptions |
| metrics |
| mutex |
| notes |
| notification_mail_list |
| notification_settings |
| notification_subscription_settings |
| notifications |
| oai_resumption_tokens |
| object_for_review_assignments |
| object_for_review_persons |
| object_for_review_settings |
| objects_for_review |
| paypal_transactions |
| pln_deposit_objects |
| pln_deposits |
| plugin_settings |
| processes |
| published_articles |
| queued_payments |
| referral_settings |
| referrals |
| review_assignments |
| review_form_element_settings |
| review_form_elements |
| review_form_responses |
| review_form_settings |
| review_forms |
| review_object_metadata |
| review_object_metadata_settings |
| review_object_type_settings |
| review_object_types |
| review_rounds |
| roles |
| rt_contexts |
| rt_searches |
| rt_versions |
| scheduled_tasks |
| section_editors |
| section_settings |
| sections |
| sessions |
| signoffs |
| site |
| site_settings |
| static_page_settings |
| static_pages |
| subscription_type_settings |
| subscription_types |
| subscriptions |
| temporary_files |
| theses |
| usage_stats_temporary_records |
| user_interests |
| user_settings |
| users |
| versions |
±--------------------------------------+
126 rows in set (0.00 sec)
mysql>
Anders
February 22, 2019, 10:36am
4
Hi Jason,
I took a guess a truncated the following three tables
| article_search_keyword_list |
| article_search_object_keywords |
| article_search_objects |
After that the upgrade completed, but I saw a lot of this:
PHP Notice: unserialize(): Error at offset 68 of 210 bytes in /var/www/html/ojs/lib/pkp/classes/db/DAO.inc.php on line 352
Is that a problem?
They also came when I ran the php tools/rebuildSearchIndex.php script.
The system appears to be running normally.
/Anders
jnugent
February 22, 2019, 4:16pm
5
Hi Anders,
Ah, yes sorry about that - and glad that the upgrade worked out okay.
Those unserialize errors might be content encoding mismatches. When you upgraded, did you maintain any UTF-8 character settings across your configuration files?
Cheers,
Jason