php v 5.6.38
When I attempt to upgrade my database on a test server I get the following issues/errors:
PHP Strict Standards: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/web/OJS311/ojs/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 386
[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]
PHP Strict Standards: Only variables should be assigned by reference in /var/web/OJS311/ojs/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
[data: dbscripts/xml/upgrade/3.0.0_adaptTimedViews.xml (skipped)]
[data: dbscripts/xml/upgrade/3.0.0_adaptReferrals.xml]
PHP Strict Standards: Only variables should be assigned by reference in /var/web/OJS311/ojs/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
[data: dbscripts/xml/upgrade/3.0.0_adaptBooksForReview.xml]
PHP Strict Standards: Only variables should be assigned by reference in /var/web/OJS311/ojs/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
[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]
PHP Strict Standards: Only variables should be assigned by reference in /var/web/OJS311/ojs/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
[data: dbscripts/xml/upgrade/3.1.1_preupdate_citations.xml]
PHP Strict Standards: Only variables should be assigned by reference in /var/web/OJS311/ojs/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
[schema: lib/pkp/xml/schema/common.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/log.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/announcements.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/scheduledTasks.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/temporaryFiles.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/metadata.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/reviews.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/reviewForms.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/controlledVocab.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/submissions.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/submissionFiles.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/notes.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/views.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/genres.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/tombstone.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/rolesAndUserGroups.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/metrics.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/views.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/libraryFiles.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[schema: lib/pkp/xml/schema/navigationMenus.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[schema: dbscripts/xml/ojs_schema.xml]
PHP Strict Standards: Only variables should be passed by reference in /var/web/OJS311/ojs/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
[data: dbscripts/xml/indexes.xml]
[code: Installer Installer::installDefaultNavigationMenus]
[code: Installer Installer::migrateStaticPagesToNavigationMenuItems]
[code: Installer Installer::migrateSRLocale]
[code: Installer Installer::migrateNOLocale]
[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]
PHP Strict Standards: Declaration of SubmissionKeywordEntryDAO::getByControlledVocabId() should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /var/web/OJS311/ojs/lib/pkp/classes/submission/SubmissionKeywordEntryDAO.inc.php on line 20
PHP Strict Standards: Declaration of SubmissionLanguageEntryDAO::getByControlledVocabId() should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /var/web/OJS311/ojs/lib/pkp/classes/submission/SubmissionLanguageEntryDAO.inc.php on line 46
PHP Strict Standards: Declaration of SubmissionAgencyEntryDAO::getByControlledVocabId() should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /var/web/OJS311/ojs/lib/pkp/classes/submission/SubmissionAgencyEntryDAO.inc.php on line 44
[data: dbscripts/xml/upgrade/3.0.0_update.xml]
[code: Installer Installer::clearDataCache]
[code: Installer Installer::migrateUserRoles]
[code: Installer Installer::fixReviewForms]
[code: Installer Installer::htmlifyEmailTemplates]
[note: docs/release-notes/README-BEACON]
[code: Installer Installer::installEmailTemplate]
[code: Installer Installer::installEmailTemplate]
[code: Installer Installer::installEmailTemplate]
[code: Installer Installer::installEmailTemplate]
[code: Installer Installer::installEmailTemplate]
[code: Installer Installer::installEmailTemplate]
[data: dbscripts/xml/upgrade/3.0.0_scheduledTasks.xml]
[code: Installer Installer::localizeCustomBlockSettings]
[code: Installer Installer::convertEditorDecisionNotes]
[code: Installer Installer::convertQueries]
PHP Strict Standards: Declaration of SubmissionFileDAO::fromRow() should be compatible with PKPSubmissionFileDAO::fromRow($row, $fileImplementation) in /var/web/OJS311/ojs/classes/article/SubmissionFileDAO.inc.php on line 23
[code: Installer Installer::migrateFiles]
Followed by LOTS of warnings similar to this:
WARNING: Unable to find a match for “122-xx-xx-SM.html” in “/var/web/OJSFiles/OJS311/files/journals/1//articles/122/”. Skipping this file.
[code: Installer Installer::convertSupplementaryFiles]
PHP Warning: copy(/var/web/OJSFiles/OJS311/files/journals/1//articles/15/attachment/15-1-98-1-13-20120514.zip): failed to open stream: No such file or directory in /var/web/OJS311/ojs/lib/pkp/classes/file/FileManager.inc.php on line 159
PHP Warning: assert(): Assertion failed in /var/web/OJS311/ojs/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php on line 123
PHP Warning: copy(/var/web/OJSFiles/OJS311/files/journals/1//articles/14/attachment/14-1-55-1-13-20120129.doc): failed to open stream: No such file or directory in /var/web/OJS311/ojs/lib/pkp/classes/file/FileManager.inc.php on line 159
PHP Warning: assert(): Assertion failed in /var/web/OJS311/ojs/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php on line 123
PHP Warning: assert(): Assertion failed in /var/web/OJS311/ojs/lib/pkp/classes/submission/PKPSubmissionFileDAO.inc.php on line 374
[code: Installer Installer::provideSupplementaryFilesForReview]
PHP Warning: copy(/var/web/OJSFiles/OJS311/files/journals/1//articles/14/submission/proof/14-12-55-1-10-20120129.doc): failed to open stream: No such file or directory in /var/web/OJS311/ojs/lib/pkp/classes/file/FileManager.inc.php on line 159
PHP Warning: assert(): Assertion failed in /var/web/OJS311/ojs/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php on line 112
PHP Warning: copy(/var/web/OJSFiles/OJS311/files/journals/1//articles/14/submission/review/14-12–1-4-20120129.doc): failed to open stream: No such file or directory in /var/web/OJS311/ojs/lib/pkp/classes/file/FileManager.inc.php on line 159
PHP Fatal error: Call to a member function getFileId() on null in /var/web/OJS311/ojs/lib/pkp/classes/submission/PKPSubmissionFileDAO.inc.php on line 1065
I had some old files that were bogus so I ran the following items to purge them before doing the update otherwise the upgrade would attempt to make false directories in the files directories:
DELETE a, c
FROM article_supplementary_files a
JOIN article_supp_file_settings c ON a.supp_id = c.supp_id
where a.article_id = ‘5’
or a.article_id =‘13’
or a.article_id =‘17’
or a.article_id =‘26’
or a.article_id =‘30’
or a.article_id =‘43’;
DELETE a from articles a where a.article_id = ‘5’
or a.article_id =‘13’
or a.article_id =‘17’
or a.article_id =‘26’
or a.article_id =‘30’
or a.article_id =‘43’;
DELETE a from article_files a where a.article_id = ‘5’
or a.article_id =‘13’
or a.article_id =‘17’
or a.article_id =‘26’
or a.article_id =‘30’
or a.article_id =‘43’;
DELETE a from article_comments a where a.article_id = ‘5’
or a.article_id =‘13’
or a.article_id =‘17’
or a.article_id =‘26’
or a.article_id =‘30’
or a.article_id =‘43’;
DELETE a from article_galleys a where a.article_id = ‘5’
or a.article_id =‘13’
or a.article_id =‘17’
or a.article_id =‘26’
or a.article_id =‘30’
or a.article_id =‘43’;
DELETE a, c
FROM article_search_objects a
JOIN article_search_object_keywords c ON a.object_id = c.object_id
where a.article_id = ‘5’
or a.article_id =‘13’
or a.article_id =‘17’
or a.article_id =‘26’
or a.article_id =‘30’
or a.article_id =‘43’
;
DELETE a from article_settings a where a.article_id = ‘5’
or a.article_id =‘13’
or a.article_id =‘17’
or a.article_id =‘26’
or a.article_id =‘30’
or a.article_id =‘43’;
DELETE a from edit_assignments a where a.article_id = ‘5’
or a.article_id =‘13’
or a.article_id =‘17’
or a.article_id =‘26’
or a.article_id =‘30’
or a.article_id =‘43’;
DELETE a from edit_decisions a where a.article_id = ‘5’
or a.article_id =‘13’
or a.article_id =‘17’
or a.article_id =‘26’
or a.article_id =‘30’
or a.article_id =‘43’;
DELETE a from referrals a where a.article_id = ‘5’
or a.article_id =‘13’
or a.article_id =‘17’
or a.article_id =‘26’
or a.article_id =‘30’
or a.article_id =‘43’;
I also ran SELECT * FROM articles a LEFT JOIN sections s ON (a.section_id = s.section_id) WHERE s.section_id IS NULL;
which gave me two article_id of 4 and 59 so I updated their section id’s
update articles set section_id = ‘1’ where article_id = ‘4’ or article_id =‘59’;
Any help would be appreciated.