@NateWr, you are funny! thanks for making my day feel better.
Anyway, I was able to remove those “file_id” by running this query:
DELETE FROM review_round_files WHERE file_id IN (2889,2928, 2954, 2912, 3192,…);
but it didn’t seem to resolve my " SQLSTATE[HY000]: General error. 1005" error above.
So I tried to convert my database engine from MyISAM to InnoDB. And the installation
went through with some newer errors.
Please see below:
[pre-install]
[load: upgrade.xml]
[version: 3.3.0.6]
[code: Installer Installer::checkPhpVersion]
[code: Installer Installer::migrateSubmissionCoverImages]
[data: dbscripts/xml/upgrade/3.2.0_preupdate_email_templates.xml]
[data: dbscripts/xml/upgrade/3.2.0_preupdate_versioning_articleGalleySettings.xml (skipped)]
[data: dbscripts/xml/upgrade/3.2.0_preupdate_versioning.xml]
[data: dbscripts/xml/upgrade/3.2.0_preupdate_last_activity.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/categories.xml]
[schema: lib/pkp/xml/schema/notes.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]
[code: Installer Installer::installDefaultNavigationMenus]
WARNING: The NavigationMenu (ContextId: 1, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
WARNING: The NavigationMenu (ContextId: 1, Title: Primary Navigation Menu, Area: primary) will be skipped because the specified area has already a NavigationMenu attached.
WARNING: The NavigationMenu (ContextId: 2, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
WARNING: The NavigationMenu (ContextId: 2, Title: Primary Navigation Menu, Area: primary) will be skipped because the specified area has already a NavigationMenu attached.
WARNING: The NavigationMenu (ContextId: 0, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
[code: Installer Installer::migrateStaticPagesToNavigationMenuItems]
[code: Installer Installer::migrateUserAndAuthorNames (skipped)]
[data: dbscripts/xml/upgrade/3.2.0_stylesheet.xml]
[data: dbscripts/xml/upgrade/3.2.0_archiving_settings.xml]
[data: dbscripts/xml/upgrade/3.2.0_update.xml]
[data: dbscripts/xml/upgrade/3.2.0_navigation_menu_items_locale_change.xml]
[code: Installer Installer::migrateSiteLocales]
[code: Installer Installer::migrateSidebarBlocks]
[code: Installer Installer::migrateSiteStylesheet]
[code: Installer Installer::migrateMetadataSettings]
[code: Installer Installer::createLicenseTerms]
[code: Installer Installer::installEmailTemplate]
[code: Installer Installer::changeUserRolesAndStageAssignmentsForStagePermitSubmissionEdit]
[data: dbscripts/xml/upgrade/3.2.0_versioning.xml]
[data: dbscripts/xml/upgrade/3.2.0_versioning_submissionCategories.xml]
[data: dbscripts/xml/upgrade/3.2.0_last_activity.xml]
[data: dbscripts/xml/upgrade/3.2.0_url_path.xml]
[code: Installer Installer::setStatsEmailSettings]
[code: Installer Installer::fixLibraryFiles]
[code: Installer Installer::installEmailTemplate]
[note: docs/release-notes/README-3.2.0]
[data: dbscripts/xml/upgrade/3.2.1_update.xml]
[code: Installer Installer::installEmailTemplate]
[migration: PKPv3_2_1SubeditorCategoriesMigration]
[note: docs/release-notes/README-3.2.1]
[migration: PKPv3_3_0UpgradeMigration]
A submission file was expected but not found at journals/1/articles/1/submission/proof/1-12-2-1-10-20090602.doc.
A submission file was expected but not found at journals/1/articles/5/submission/proof/5-12-10-1-10-20090623.doc.
A submission file was expected but not found at journals/1/articles/9/submission/proof/9-12-21-1-10-20090723.doc.
A submission file was expected but not found at journals/1/articles/26/submission/review/attachment/26-1-121-1-5-20091227.docx.
A submission file was expected but not found at journals/1/articles/26/submission/review/attachment/26-1-184-1-5-20100204.doc.
A submission file was expected but not found at journals/1/articles/47/submission/copyedit/47-1-195-1-9-20100305.doc.
A submission file was expected but not found at journals/1/articles/28/submission/review/attachment/28-1-200-1-5-20100404.docx.
A submission file was expected but not found at journals/1/articles/49/submission/copyedit/49-1-208-1-9-20100502.doc.
A submission file was expected but not found at journals/1/articles/51/submission/copyedit/51-1-221-1-9-20100518.doc.
A submission file was expected but not found at journals/1/articles/53/submission/copyedit/53-1-236-1-9-20100615.doc.
A submission file was expected but not found at journals/1/articles/53/submission/copyedit/53-1-236-2-9-20100616.doc.
A submission file was expected but not found at journals/1/articles/28/submission/review/attachment/28-1-240-1-5-20100624.doc.
A submission file was expected but not found at journals/1/articles/63/submission/copyedit/63-1-285-1-9-20100708.doc.
A submission file was expected but not found at journals/1/articles/68/submission/review/attachment/68-1-312-1-5-20100827.doc.
A submission file was expected but not found at journals/1/articles/74/submission/copyedit/74-1-323-1-9-20100908.doc.
A submission file was expected but not found at journals/1/articles/74/submission/proof/74-12-324-1-10-20100909.docx.
A submission file was expected but not found at journals/1/articles/68/submission/review/attachment/68-1-327-1-5-20100914.docx.
A submission file was expected but not found at journals/1/articles/67/submission/review/attachment/67-1-328-1-5-20100920.doc.
A submission file was expected but not found at journals/1/articles/67/submission/review/attachment/67-1-332-1-5-20100925.doc.
A submission file was expected but not found at journals/1/articles/82/submission/proof/82-12-364-2-10-20101014.doc.
A submission file was expected but not found at journals/1/articles/70/submission/review/attachment/70-1-403-1-5-20101122.docx.
A submission file was expected but not found at journals/1/articles/86/submission/review/attachment/86-1-433-1-5-20101207.docx.
A submission file was expected but not found at journals/1/articles/86/submission/review/attachment/86-1-450-2-5-20110114.doc.
A submission file was expected but not found at journals/1/articles/86/submission/review/attachment/86-1-450-3-5-20110114.doc.
A submission file was expected but not found at journals/1/articles/82/submission/review/attachment/82-1-472-1-5-20110307.doc.
A submission file was expected but not found at journals/1/articles/82/submission/review/attachment/82-1-493-1-5-20110407.doc.
A submission file was expected but not found at journals/1/articles/98/submission/review/attachment/98-1-534-1-5-20110531.doc.
A submission file was expected but not found at journals/1/articles/99/submission/review/attachment/99-1-536-1-5-20110531.docx.
A submission file was expected but not found at journals/1/articles/98/submission/review/attachment/98-1-537-1-5-20110531.docx.
ETC
.
.
A submission file was expected but not found at journals/1/articles/358/submission/review/attachment/358-1-2541-1-5-20161230.doc.
A submission file was expected but not found at journals/1/articles/354/submission/review/attachment/354-1-2558-1-5-20170113.docx.
A submission file was expected but not found at journals/1/articles/357/submission/review/attachment/357-1-2611-1-5-20170306.docx.
A submission file was expected but not found at journals/1/articles/357/submission/review/attachment/357-1-2612-1-5-20170306.docx.
A submission file was expected but not found at journals/1/articles/387/submission/copyedit/387-1-2631-1-9-20170318.docx.
A submission file was expected but not found at journals/1/articles/371/attachment/371-1-2648-1-13-20170418.doc.
A submission file was expected but not found at journals/1/articles/371/attachment/371-1-2649-1-13-20170418.doc.
A submission file was expected but not found at journals/1/articles/371/attachment/371-1-2650-1-13-20170418.doc.
A submission file was expected but not found at journals/1/articles/371/attachment/371-1-2651-1-13-20170419.doc.
A submission file was expected but not found at journals/1/articles/372/attachment/372-1-2654-1-13-20170420.doc.
A submission file was expected but not found at journals/1/articles/372/attachment/372-1-2655-1-13-20170420.doc.
A submission file was expected but not found at journals/1/articles/388/submission/fairCopy/388-1-2656-1-7-20170421.docx.
A submission file was expected but not found at journals/1/articles/390/submission/review/390-1-2658-1-4-20170424.docx.
A submission file was expected but not found at journals/1/articles/373/submission/review/revision/373-1-2659-1-15-20170424.docx.
A submission file was expected but not found at journals/1/articles/352/submission/fairCopy/352-1-2660-1-7-20170424.docx.
A submission file was expected but not found at journals/1/articles/352/attachment/352-1-2661-1-13-20170424.docx.
A submission file was expected but not found at journals/1/articles/378/attachment/378-1-2663-1-13-20170425.docx.
A submission file was expected but not found at journals/1/articles/534/submission/534-1-3685-1-2-20191121.txt.
A submission file was expected but not found at journals/1/articles/534/submission/534-1-3685-2-2-20191121.txt.
A submission file was expected but not found at journals/1/articles/534/submission/534-1-3687-1-2-20191121.txt.
A submission file was expected but not found at journals/1/articles/599/submission/599-12-4288-1-2-20201006.doc.
Removing orphaned review_files entry with review_id ID 320 and submission_file_id 2970
Removing orphaned review_files entry with review_id ID 321 and submission_file_id 2970
Removing orphaned review_files entry with review_id ID 322 and submission_file_id 2970
Removing orphaned review_files entry with review_id ID 328 and submission_file_id 3096
Removing orphaned review_files entry with review_id ID 333 and submission_file_id 3096
[migration: OJSv3_3_0UpgradeMigration]
[note: docs/release-notes/README-3.3.0]
[code: Installer Installer::addPluginVersions]
[post-install]
Release Notes
OJS 3.2.0-1 Release Notes
Git tag: 3_2_0-1
Release date: March 20, 2020
Bug Fixes (-1 build)
#5652: Clean up status code in QuickSubmit form
#5646: Call to undefined method AuthorDAO::getBySubmissionId()
#5600: pkp-native.xml uses publication element instead of pkppublication
#5643: Error in journal settings form when locale active in Form but not UI
#5536: Plugins/themes to package and release before 3.2
#5636: Handler adjustments for new versions
#5635: Manager’s Table of Contents grid does not list unpublished submissions
#5634: Resolve OJS 2.x to 3.2 upgrade issues
#5605: Top right link to profile is invisible (text in white, over a white background)
#5632: [OMP] Chapter PDF will not display
#5628: Supporting Agencies field does not display in submission metadata form
#5626: Upgrade error: Duplicate entry ‘xxx-yyy’ for key ‘citations_publication_seq’
#5621: Article report plugin references missing function
#5623: Raw citations should be escaped on the front-end
#5597: Native import/export plugin adds a blank citation when importing submissions with citations
#5602: JournalManager/Author metadata edit error: “Please enter the references.”
#5589: [OJS] PostgreSQL can not recognize update SQL queries
#5612: Generate site minimum-length password
#5267: Automatic password generation doesn’t respect site minimum password length
#5591: Author lists are not sorted by sequence
#5584: Enable/disable journal setting not available in 3.2.0
#5571: Cannot Display Sidebar in ojs 3.2.0.0
#5582: PHP error “Can’t inherit abstract function SchemaDAO::newDataObject()”
#5576: Can’t upload image in user profile bio
#5570: Fix Lens galley plugin
#4195: references native import
#5575: Can’t download supplementary galleys when publication has urlPath
Release date: February 28, 2020
New Features
#2072: [OJS] Versioning for published articles
#2096: Add support for rtl locales
#2438: [OJS] Editors should be able to add attachments to the Editorial Decision message
#2508: Improve editor control over reviews
#2820: Improve internal submission data reporting
#2906: Improve Email Templates View
#3594: Implement form support in Vue.js/REST API
#3673: Article usage stats
#3758: Selectively permit author metadata changes after submission
#3803: integrate new Crossref deposit and submissionDownload API
#3817: Add option to display journal summary on homepage
#4149: Enrich OAI-PMH options for journals that do not publish online
#4158: Allow JEs to assemble published articles into thematic collections
#4683: Add option in default theme to use homepage image as header background
#4772: Permit the “merge users” CLI tool to handle multiple users at once
#4779: Replace bespoke translation toolset with more standards-based options
#4844: Implement internal Editorial Report UI and algorithms
#4867: Support publications/versioning for DOIs and verify depositing
#4870: Support versioning in the reader interface
#5085: Add proxy support to plugin gallery
#5277: Add “Obsolete version” notice to PDF viewer when new version available
Bug Fixes
#1116: setLocale ignores source parameter if HTTP_REFERER exists
#1375: [OJS] Updating issue without volume results on 0 on database
#1403: Redirect to the current page after Login As
#1908: Fix/resolve LOCKSS registration/manifest/plugin
#2071: [OJS3] Create new issue stalls when volume number is not an integer
#2294: [OJS] Returning to search from a search result leads to an expired document
#2353: Test migration of ADODB to Composer dependency
#2428: [OJS] CSRF token validity time (one hour) breaks the review form
#2617: Add counts of submissions to submission tabs and list filters
#3248: [OJS] submission emails: signature information is slightly duplicated
#3330: [OJS] Payments need to be enabled to change the length of journal embargo
#3340: Add timestamp to CSS and JS files for when they are built
#3381: Problems scrolling PDF/HTML galleys in iOS
#3386: [OJS 3.1] Declined submissions not appropriately highlighted as such
#3439: [OJS] Institutional Subscription creation form “domain” field requirements need minor tweaking
#3535: Section settings heading “Indexing” is not clear to end-users
#3691: Add default styling for HTML galleys
#3697: Improve / correct manuscript status in submission list for editors
#3770: Reduce the number of new submission notification emails for editors, and simplify their management
#3784: consider site primary locale and the submission locale change
#3831: Can’t override core templates
#3910: Section editors can not access comments to editor discussion
#3948: [OJS] webfeed Plugin rss2 missing XML namespace and date time issue
#4021: Article subtitles not showing in “how to cite”
#4054: Overridden plugin templates in theme not shown in child theme
#4097: [OJS] Fix for #3705 breaks archives with PostgreSQL
#4164: Support generating DMARC compliant mails
#4168: Add filter by last modified more than X days ago to submissions lists
#4204: Add hostname checking for ReCAPTCHA
#4213: After thanking, reviewer decisions is not seen on Review page
#4214: [OJS 3.1.1.4] Translation keys might be confused for some locales (navigation.submissions & about.submissions)
.
.
.
#5550: Fatal error due to changes in SettingsDAO
#5553: Abstract length error message includes Array instead of correct length
#5560: Files for old versions don’t load
#5563: Possible to access unpublished articles when not logged in
#5569: Fix OJS 2.x to 3.x upgrade
OJS 3.2.1-3 Release Notes
Git tag: 3_2_1-3
Release date: January 22, 2021
Configuration Changes
See config.TEMPLATE.inc.php for a description and examples of all supported
configuration parameters.
New config.inc.php parameters:
- database.collation - The character set collation to use in database
queries. Default: utf8_general_ci
- email.smtp_suppress_cert_check - True if PHPMailer’s certificate check
is to be disabled. Not recommended unless you’re sure. Default: Off
- curl.cainfo - Path to Certificate Authority (CA) bundle.
3.2.1-3 Build
#6644: Fatal error if notifications are blocked for EditorialReportNotificationManager
#6632: Update Illuminate Database library for GHSA-3p32-j457-pg5x
#6620: WebFeed plugin missing restriction to published content
#6548: User issue payment unlocks issue globally for users who aren’t logged in
#6529: Author can not upload revisions when decision is to resubmit for review
#6510: Non-expiring institutional subscription can’t be added
#6495: Incorrect URLs in default context settings
#6473: Allow for access to public Library Files without forcing a download
#6467: “Reload defaults” for language invalidates $contextPath variable
#6462: Inconsistency in JWT (API key) encoding/decoding
#6421: Dependent file upload fails when confirm revision is detected
#6389: Trying to register an article with the DOAJ plugin throws an error : new DOAJ API version
#6344: Remove script host from smarty variables
#6320: [OJS] CAST AS CHAR i postgres
#6189: [OJS] Problem when submitting reviews
#6060: If a title prefix is given for a single locale, it is shown with all article title translations
#4414: Context path property creates conflict when disable_path_info is enabled
3.2.1-2 Build
#2580: Correct outdated reference to geo IP tool path
#4991: Add Category to article page in OJS
#5445: Test licenseUrl context setting
#5565: Allow editors and editorial assistants to preview an article before it is published
#5592: [OJS] Block plugins and cacheing problem
#6029: Report Generator doesn’t return any results when custom range is selected with a single day
#6056: [OPS] Version number showing Publication ID for authors
#6064: [OJS] Text color does not respond to background color selection on mobile
#6067: Submission Checklist - Reordering doesn’t save
#6069: package-lock.json contains wrong version number
#6084: Announcement emails sent blank after upgrade
#6102: Submission::getSectionTitle doesn’t return any value
#6105: Allow capital letters in context urlPath
#6107: “Omit the title of this section from the issue’s Table of Contents” section option does not work
#6111: SQL typo in “browse by authors” feature
#6115: Enable “download all files” in production ready files grid
#6120: Internal Review queries are placed in External Review
#6134: The statistics notification is sent to roles that have no access to the interface
#6301: Add indexes for search performance
#6330: Lens Galley XML views not tracked in usage statistics
3.2.1-1 Build
#6045: Permit database collation configuration
#6041: License override formatting error
#6035: Plugin install does not work across filesystems
#6033: Announcements can be viewed even when disabled
#6007: User roles can be passed to the browser as an object instead of array
New Features
#5886: OMP site wide search
#5784: [OMP] Site index should list all presses
#5744: Add Noto font for Arabic characters
#5703: Improve upgrade performance
#5694: Allow subeditors to be assigned to Categories
#5601: Add range slider for filter by last activity in submissions list
#5190: Add TITLE parameter to IFRAME of article galley view
#5177: Issue archive pages should add headings to issue titles
#4888: Write integration tests for versioning features
#3698: Support a “draft” option for reviews
Bug Fixes
#6026: Submission deletion can delete author records in other submissions
#6022: PostgreSQL upgrade to 3.2.0 resets all submissions to unpublished
#6000: Undefined const SCHEMA_PUBLICATION during upgrade
#5977: Fatal error viewing HTML publication format in OMP
#5974: TinyMCE can not be loaded in sr_RS@cyrillic locale
#5967: SQL error on 3.2.0->3.2.1RC upgrade
#5961: enabling crossrefReferenceLinking (even master branch) makes doi disappear
#5933: [OPS] Editorial Statistics “Active Submissions” don’t match actual number
#5923: PostgreSQL 12 not properly supported
#5920: Native ImportExport Plugin: Importing a localized publication causes an error
#5907: CrossRefExportPlugin Article Search not filtering by Status
#5903: Reorder OPS archive/browse handlers
#5876: OJS3.2 Editorial activity stats counting submissions from removed journals
#5872: Update Cypress and vue-cli to address warnings
#5869: Clean up plugin installation error handling
#5862: Resolve double slash in file paths during upgrade
#5860: Multilingual form fields do not show primary locale on initial load
#5856: Review Form not getting the correct title and description
#5837: Publication and Submission State inconsistency
#5833: [OMP] Order catalog by series position leads to database error
#5813: Logged out users directed to site homepage instead of journal homepage when logo is present
#5801: Recommend by Author Plugin duplicates entries
#5796: Metadata sections in submission form
#5791: Vue js error after choosing a file for uploading
#5789: H1 for screen readers not available in Site level if site logo is given
#5781: Optionally suppress SMTP authentication in PHPMailer
#5698: Update the citation library to solving the citation problem.
#5695: OJS - Extra space below empty submission list
#5693: ValidationFactory reports required fields with value “0” as invalid
#5640: Language installation features hidden from single-journal installations
#5633: FormComponent subclasses, even when invoked via the API, require CSRF tokens
#5631: Mismatch between datePublished and issue scheduling can cause problems
#5630: Unscheduling a publication does not update the issue scheduling field
#5617: Themes shown when installed, even if they are not enabled
#5585: Update syntax for draggable options
#5533: Unclear language for setting to allow participants to edit metadata
#5532: Editors fail to schedule for publication
#5373: Unported CC licenses 3.0
#5288: Performance issue using LIMIT and OFFSET in search users query
#5273: User validation email references {$contextName}, which is not resolved before sending
#5265: Crossref error message is not translated
#5240: Skip links and anchors in the default theme should appear within landmarks
#5186: Add aria-required to register and login forms
#5176: Sidebar blocks should always have a heading and section
#5175: Fix use of
in header
#5095: Workflow participants receive more than one email about the same thing
#5061: [OJS 3.1.2-1] Crossref module: Language of all metadata EXCEPT author names depends on submission language (author names depend on locale chosen)
#4746: Announcement notification email should include the announcement content
#4042: Editorial history should save the datestamp when a new review round starts
OJS 3.3.0 Release Notes
Git tag: 3_3_0-5
Release date: April 7, 2021
Configuration Changes
See config.TEMPLATE.inc.php for a description and examples of all supported
configuration parameters.
- The proxy configuration settings have changed. Please review the [proxy]
section in config.TEMPLATE.inc.php and adapt your settings in config.inc.php
as needed.
- The db.persistent option for persistent database connections has been removed.
- The db.collation option for configuring a database connection collation has
been added (default: utf8_general_ci)
New config.inc.php parameters added for OAuth-based SMTP authorization:
(see Using Gmail with XOAUTH2 · PHPMailer/PHPMailer Wiki · GitHub)
- email.smtp_authtype: See PHPMailer’s AuthType setting
- email.smtp_oauth_provider
- email.smtp_oauth_email
- email.smtp_oauth_clientid
- email.smtp_oauth_clientsecret
- email.smtp_oauth_refreshtoken
3.3.0-6 Build
#6986: HTML entities displayed in journal title by citationStyleLanguage plugin
.
.
.
#6232 #6632 #6378: Update 3rd-party dependencies
#6633: Entering a space in journal path breaks site
#6634: Block names aren’t being updated to the lowercase during OJS upgrade
#6638: The fileStages filter of the submission files API is ignored for managers
#6654: The cancel button at the “Change Password” has no purpose
#6668: Public message when not accepting submissions is confusing
#6671: no router object when executing scheduled tasks
#6681: GET request to /contexts API endpoint causes 500 error
Successfully upgraded to version 3.3.0.6
I also found another PHP error after checking the new version in browser,
Please see below
any suggestion?
thanks
-Ptran
