Upgrade 2.4.8.1 to 3.1.2-4

Software Support
1

Dear all,

I am trying to upgrade my ojs from 2.4.8.1 to 3.1.2-4. I have warnings and errors that I don’t understand and I don’t kwow how to proceed.

  1. Some files don’t exist. I think there are records in the database but not in the data folder:
    [27-Dec-2019 23:49:31 UTC] WARNING: Unable to find a match for “40-172-1-RV.pdf” in “/home/_ojsdata/journals/11//articles/40/”. Skipping this file.
    [27-Dec-2019 23:49:31 UTC] WARNING: Unable to find a match for “41-175-1-RV.pdf” in “/home/_ojsdata/journals/11//articles/41/”. Skipping this file.

  2. Error with unserialize funtion.
    [27-Dec-2019 23:56:56 UTC] PHP Notice: unserialize(): Error at offset 3882 of 4099 bytes in /_ojs3/lib/pkp/classes/db/DAO.inc.php on line 352
    [27-Dec-2019 23:56:57 UTC] PHP Notice: unserialize(): Error at offset 72 of 3768 bytes in /_ojs3/lib/pkp/classes/db/DAO.inc.php on line 352

  3. Error with getFileId() funtion:

[28-Dec-2019 01:09:36 UTC] PHP Warning: assert(): assert(is_readable($sourceFile)) failed in /_ojs3/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php on line 112
[28-Dec-2019 01:09:36 UTC] PHP Warning: copy(_ojsdata/journals/7//articles/96/submission/proof/96-38-268-1-10-20111118.doc): failed to open stream: No such file or directory in /_ojs3/lib/pkp/classes/file/FileManager.inc.php on line 162
[28-Dec-2019 01:09:36 UTC] PHP Fatal error: Uncaught Error: Call to a member function getFileId() on null in /_ojs3/lib/pkp/classes/file/SubmissionFileManager.inc.php:184

Thank you very much. I really appreciate your help.

2

Dear all,

I have solved the unserialize() problems but I have the error with getFileId(). Any suggestions?

thank you very much

[03-Jan-2020 17:34:30 UTC] PHP Fatal error: Uncaught Error: Call to a member function getFileId() on null in /home/_ojs3/lib/pkp/classes/file/SubmissionFileManager.inc.php:184
Stack trace:
#0 /home/_ojs3/classes/install/Upgrade.inc.php(1477): SubmissionFileManager->copyFileToFileStage(‘268’, 1, 4, NULL, true)
#1 /home/_ojs3/lib/pkp/classes/install/Installer.inc.php(421): Upgrade->provideSupplementaryFilesForReview(Object(Upgrade), Array)
#2 /home/_ojs3/lib/pkp/classes/install/Installer.inc.php(265): Installer->executeAction(Array)
#3 /home/_ojs3/lib/pkp/classes/install/Installer.inc.php(186): Installer->executeInstaller()
#4 /home/_ojs3/lib/pkp/classes/cliTool/UpgradeTool.inc.php(88): Installer->execute()
#5 /home/_ojs3/lib/pkp/classes/cliTool/UpgradeTool.inc.php(64): UpgradeTool->upgrade()
#6 /home/_ojs3/tools/upgrade.php(34): UpgradeTool- in /home/_ojs3/lib/pkp/classes/file/SubmissionFileManager.inc.php on line 184

3

Dear all,

I solved the missing files, but now I don’t know how to solve this error? Anyone could help me?

thank you very much

[09-Jan-2020 13:54:30 UTC] PHP Warning: assert(): assert($previousFilePath != $targetFilePath && !file_exists($targetFilePath)) failed in /home/_ojs3/lib/pkp/classes/submission/SubmissionFileDAO.inc.php on line 374
[09-Jan-2020 13:54:30 UTC] PHP Warning: assert(): assert($previousFilePath != $targetFilePath && !file_exists($targetFilePath)) failed in /home/_ojs3/lib/pkp/classes/submission/SubmissionFileDAO.inc.php on line 374
[09-Jan-2020 13:54:39 UTC] PHP Fatal error: Uncaught Error: Call to a member function getFullName() on null in /home/_ojs3/lib/pkp/classes/submission/reviewAssignment/ReviewAssignmentDAO.inc.php:480
Stack trace:
#0 /home/_ojs3/lib/pkp/classes/submission/reviewAssignment/ReviewAssignmentDAO.inc.php(69): ReviewAssignmentDAO->_fromRow(Array)
#1 /home/_ojs3/lib/pkp/classes/submission/reviewAssignment/ReviewAssignmentDAO.inc.php(217): ReviewAssignmentDAO->_getReviewAssignmentsArray(‘SELECT r.*, r2…’, Array)
#2 /home/_ojs3/classes/install/Upgrade.inc.php(1482): ReviewAssignmentDAO->getBySubmissionId(‘251’, 165, 3)
#3 /home/_ojs3/lib/pkp/classes/install/Installer.inc.php(421): Upgrade->provideSupplementaryFilesForReview(Object(Upgrade), Array)
#4 /home/_ojs3/lib/pkp/classes/install/Installer.inc.php(265): Installer->executeAction(Array)
#5 /home/_ojs3/lib/pkp/classes/ins in /home/_ojs3/lib/pkp/classes/submission/reviewAssignment/ReviewAssignmentDAO.inc.php on line 480

4

Hi @ipa,

I suspect your review_assignments table contains a reference to a reviewer_id that does not exist in the users table.

Regards,
Alec Smecher
Public Knowledge Project Team

5

Thank you @asmecher,

I think that I solved it bu now I have the new message error:
"[code: Installer Installer::convertCommentsToEditor]
[note: docs/release-notes/README-3.0]
[note: docs/release-notes/README-3.0.1]
[data: dbscripts/xml/upgrade/3.0.2_update.xml]
[note: docs/release-notes/README-3.0.2]

[code: Installer Installer::moveReviewerFiles]

There are no readable files in this directory tree. Are safe mode or open_basedir active?

"

I think the folder have already the readable permissions.

thank you

6

Hi @ipa,

Could you post this as a new topic? That’ll help keep the forum organized. Please include what you’ve tried specifically for file permissions.

Regards,
Alec Smecher
Public Knowledge Project Team

7

Hi @asmecher!

I am sorry to introduce a new topic. I think that I have solved the problem due to error values in the database, the upgrade have been done successfully

thank you very much, I really appreciate your dedication.