Error While Database upgrade from 2.4.8 to 3.1.1.2

mbabaei · August 22, 2018, 7:22am

Hi @bozana , @asmecher
When trying to update my database from 2.4.8 to 3.1.1.2 with command line “php tools/upgrade.php upgrade”
I get this error

 [code: Installer Installer::provideSupplementaryFilesForReview]
PHP Warning:  copy(/media/ojs/B42C62B32C626FF2/files-backup/files/journals/16//articles/732/submission/732-120-2058-1-2-20090411.doc): failed to open stream: No such file or directory in /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/file/FileManager.inc.php on line 159
PHP Stack trace:
PHP   1. {main}() /media/ojs/B42C62B32C626FF2/convert2/tools/upgrade.php:0
PHP   2. UpgradeTool->execute() /media/ojs/B42C62B32C626FF2/convert2/tools/upgrade.php:34
PHP   3. UpgradeTool->upgrade() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/cliTool/UpgradeTool.inc.php:64
PHP   4. Installer->execute() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/cliTool/UpgradeTool.inc.php:88
PHP   5. Installer->executeInstaller() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:186
PHP   6. Installer->executeAction() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:265
PHP   7. call_user_func:{/media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421}() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421
PHP   8. Upgrade->provideSupplementaryFilesForReview() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421
PHP   9. SubmissionFileManager->copyFileToFileStage() /media/ojs/B42C62B32C626FF2/convert2/classes/install/Upgrade.inc.php:1493
PHP  10. FileManager->copyFile() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/file/SubmissionFileManager.inc.php:182
PHP  11. copy() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/file/FileManager.inc.php:159

Warning: copy(/media/ojs/B42C62B32C626FF2/files-backup/files/journals/16//articles/732/submission/732-120-2058-1-2-20090411.doc): failed to open stream: No such file or directory in /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/file/FileManager.inc.php on line 159

Call Stack:
    0.0003     235552   1. {main}() /media/ojs/B42C62B32C626FF2/convert2/tools/upgrade.php:0
    4.3367   12435952   2. UpgradeTool->execute() /media/ojs/B42C62B32C626FF2/convert2/tools/upgrade.php:34
    4.3367   12436136   3. UpgradeTool->upgrade() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/cliTool/UpgradeTool.inc.php:64
    5.7144   15770488   4. Installer->execute() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/cliTool/UpgradeTool.inc.php:88
    6.0447   16099736   5. Installer->executeInstaller() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:186
13732.5519   33897160   6. Installer->executeAction() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:265
13732.5519   33897696   7. call_user_func:{/media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421}() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421
13732.5519   33898088   8. Upgrade->provideSupplementaryFilesForReview() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421
13733.4987   35507552   9. SubmissionFileManager->copyFileToFileStage() /media/ojs/B42C62B32C626FF2/convert2/classes/install/Upgrade.inc.php:1493
13733.5056   35511984  10. FileManager->copyFile() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/file/SubmissionFileManager.inc.php:182
13733.5063   35512240  11. copy() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/file/FileManager.inc.php:159

PHP Warning:  assert(): Assertion failed in /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php on line 112
PHP Stack trace:
PHP   1. {main}() /media/ojs/B42C62B32C626FF2/convert2/tools/upgrade.php:0
PHP   2. UpgradeTool->execute() /media/ojs/B42C62B32C626FF2/convert2/tools/upgrade.php:34
PHP   3. UpgradeTool->upgrade() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/cliTool/UpgradeTool.inc.php:64
PHP   4. Installer->execute() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/cliTool/UpgradeTool.inc.php:88
PHP   5. Installer->executeInstaller() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:186
PHP   6. Installer->executeAction() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:265
PHP   7. call_user_func:{/media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421}() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421
PHP   8. Upgrade->provideSupplementaryFilesForReview() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421
PHP   9. SubmissionFileManager->copyFileToFileStage() /media/ojs/B42C62B32C626FF2/convert2/classes/install/Upgrade.inc.php:1493
PHP  10. PKPSubmissionFileDAO->insertObject() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/file/SubmissionFileManager.inc.php:185
PHP  11. SupplementaryFileDAODelegate->insertObject() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/submission/PKPSubmissionFileDAO.inc.php:310
PHP  12. SubmissionFileDAODelegate->insertObject() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/submission/SupplementaryFileDAODelegate.inc.php:36
PHP  13. assert() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php:112

Warning: assert(): Assertion failed in /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php on line 112

Call Stack:
    0.0003     235552   1. {main}() /media/ojs/B42C62B32C626FF2/convert2/tools/upgrade.php:0
    4.3367   12435952   2. UpgradeTool->execute() /media/ojs/B42C62B32C626FF2/convert2/tools/upgrade.php:34
    4.3367   12436136   3. UpgradeTool->upgrade() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/cliTool/UpgradeTool.inc.php:64
    5.7144   15770488   4. Installer->execute() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/cliTool/UpgradeTool.inc.php:88
    6.0447   16099736   5. Installer->executeInstaller() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:186
13732.5519   33897160   6. Installer->executeAction() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:265
13732.5519   33897696   7. call_user_func:{/media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421}() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421
13732.5519   33898088   8. Upgrade->provideSupplementaryFilesForReview() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421
13733.4987   35507552   9. SubmissionFileManager->copyFileToFileStage() /media/ojs/B42C62B32C626FF2/convert2/classes/install/Upgrade.inc.php:1493
13733.5070   35511960  10. PKPSubmissionFileDAO->insertObject() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/file/SubmissionFileManager.inc.php:185
13733.5071   35512096  11. SupplementaryFileDAODelegate->insertObject() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/submission/PKPSubmissionFileDAO.inc.php:310
13733.5071   35512096  12. SubmissionFileDAODelegate->insertObject() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/submission/SupplementaryFileDAODelegate.inc.php:36
13733.5152   35516272  13. assert() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php:112

PHP Warning:  copy(/media/ojs/B42C62B32C626FF2/files-backup/files/journals/16//articles/732/submission/review/732-120--1-4-20090411.doc): failed to open stream: No such file or directory in /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/file/FileManager.inc.php on line 159
PHP Stack trace:
PHP   1. {main}() /media/ojs/B42C62B32C626FF2/convert2/tools/upgrade.php:0
PHP   2. UpgradeTool->execute() /media/ojs/B42C62B32C626FF2/convert2/tools/upgrade.php:34
PHP   3. UpgradeTool->upgrade() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/cliTool/UpgradeTool.inc.php:64
PHP   4. Installer->execute() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/cliTool/UpgradeTool.inc.php:88
PHP   5. Installer->executeInstaller() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:186
PHP   6. Installer->executeAction() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:265
PHP   7. call_user_func:{/media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421}() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421
PHP   8. Upgrade->provideSupplementaryFilesForReview() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421
PHP   9. SubmissionFileManager->copyFileToFileStage() /media/ojs/B42C62B32C626FF2/convert2/classes/install/Upgrade.inc.php:1493
PHP  10. PKPSubmissionFileDAO->insertObject() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/file/SubmissionFileManager.inc.php:185
PHP  11. SupplementaryFileDAODelegate->insertObject() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/submission/PKPSubmissionFileDAO.inc.php:310
PHP  12. SubmissionFileDAODelegate->insertObject() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/submission/SupplementaryFileDAODelegate.inc.php:36
PHP  13. FileManager->copyFile() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php:113
PHP  14. copy() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/file/FileManager.inc.php:159

Warning: copy(/media/ojs/B42C62B32C626FF2/files-backup/files/journals/16//articles/732/submission/review/732-120--1-4-20090411.doc): failed to open stream: No such file or directory in /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/file/FileManager.inc.php on line 159

Call Stack:
    0.0003     235552   1. {main}() /media/ojs/B42C62B32C626FF2/convert2/tools/upgrade.php:0
    4.3367   12435952   2. UpgradeTool->execute() /media/ojs/B42C62B32C626FF2/convert2/tools/upgrade.php:34
    4.3367   12436136   3. UpgradeTool->upgrade() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/cliTool/UpgradeTool.inc.php:64
    5.7144   15770488   4. Installer->execute() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/cliTool/UpgradeTool.inc.php:88
    6.0447   16099736   5. Installer->executeInstaller() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:186
13732.5519   33897160   6. Installer->executeAction() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:265
13732.5519   33897696   7. call_user_func:{/media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421}() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421
13732.5519   33898088   8. Upgrade->provideSupplementaryFilesForReview() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421
13733.4987   35507552   9. SubmissionFileManager->copyFileToFileStage() /media/ojs/B42C62B32C626FF2/convert2/classes/install/Upgrade.inc.php:1493
13733.5070   35511960  10. PKPSubmissionFileDAO->insertObject() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/file/SubmissionFileManager.inc.php:185
13733.5071   35512096  11. SupplementaryFileDAODelegate->insertObject() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/submission/PKPSubmissionFileDAO.inc.php:310
13733.5071   35512096  12. SubmissionFileDAODelegate->insertObject() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/submission/SupplementaryFileDAODelegate.inc.php:36
13733.5153   35516176  13. FileManager->copyFile() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php:113
13733.5154   35516464  14. copy() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/file/FileManager.inc.php:159

PHP Fatal error:  Call to a member function getFileId() on null in /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/submission/PKPSubmissionFileDAO.inc.php on line 1029
PHP Stack trace:
PHP   1. {main}() /media/ojs/B42C62B32C626FF2/convert2/tools/upgrade.php:0
PHP   2. UpgradeTool->execute() /media/ojs/B42C62B32C626FF2/convert2/tools/upgrade.php:34
PHP   3. UpgradeTool->upgrade() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/cliTool/UpgradeTool.inc.php:64
PHP   4. Installer->execute() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/cliTool/UpgradeTool.inc.php:88
PHP   5. Installer->executeInstaller() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:186
PHP   6. Installer->executeAction() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:265
PHP   7. call_user_func:{/media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421}() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421
PHP   8. Upgrade->provideSupplementaryFilesForReview() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421
PHP   9. SubmissionFileManager->copyFileToFileStage() /media/ojs/B42C62B32C626FF2/convert2/classes/install/Upgrade.inc.php:1493
PHP  10. PKPSubmissionFileDAO->insertObject() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/file/SubmissionFileManager.inc.php:185
PHP  11. PKPSubmissionFileDAO->_castToDatabase() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/submission/PKPSubmissionFileDAO.inc.php:315

Fatal error: Call to a member function getFileId() on null in /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/submission/PKPSubmissionFileDAO.inc.php on line 1029

Call Stack:
    0.0003     235552   1. {main}() /media/ojs/B42C62B32C626FF2/convert2/tools/upgrade.php:0
    4.3367   12435952   2. UpgradeTool->execute() /media/ojs/B42C62B32C626FF2/convert2/tools/upgrade.php:34
    4.3367   12436136   3. UpgradeTool->upgrade() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/cliTool/UpgradeTool.inc.php:64
    5.7144   15770488   4. Installer->execute() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/cliTool/UpgradeTool.inc.php:88
    6.0447   16099736   5. Installer->executeInstaller() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:186
13732.5519   33897160   6. Installer->executeAction() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:265
13732.5519   33897696   7. call_user_func:{/media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421}() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421
13732.5519   33898088   8. Upgrade->provideSupplementaryFilesForReview() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/install/Installer.inc.php:421
13733.4987   35507552   9. SubmissionFileManager->copyFileToFileStage() /media/ojs/B42C62B32C626FF2/convert2/classes/install/Upgrade.inc.php:1493
13733.5070   35511960  10. PKPSubmissionFileDAO->insertObject() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/file/SubmissionFileManager.inc.php:185
13733.5218   35513088  11. PKPSubmissionFileDAO->_castToDatabase() /media/ojs/B42C62B32C626FF2/convert2/lib/pkp/classes/submission/PKPSubmissionFileDAO.inc.php:315

Please Help to solve this error
Thanks In advanced
Best Regards

mbabaei · August 25, 2018, 2:49am

Is there anybody here?
please help me …

asmecher · August 27, 2018, 7:40pm

Hi all,

Regarding:

Call to a member function getFileId() on null in /ojs_temp/rc-3.1.1/lib/pkp/classes/submission/PKPSubmissionFileDAO.inc.php on line 1029

According to Change galley PDF published OJS 3.1.x - #8 by marc, reviewing the file permissions and re-running the upgrade corrected the issue.

Regards,
Alec Smecher
Public Knowledge Project Team

mbabaei · August 30, 2018, 7:31pm

@asmecher @bozana
Finally after debug upgrade process i find that in FileManager.inc.php line 159, when its want run this line

if (copy($source, $dest))
		return $this->setMode($dest, FILE_MODE_MASK);
	return false;

return false because there isn’t file in $source address value
so i can add if file exist in $source then run such code but i want know that why there isn’t this file and its want copy that?

asmecher · September 14, 2018, 9:43am

Hi @mbabaei,

It sounds like there’s a file missing in your OJS 2.4.8 installation. Usually you’ll get a warning during the upgrade process when that’s the case – but I’d suggest either putting a dummy file in place (if you can’t find the file that’s supposed to be there) or, better yet, identify the missing file and restore it.

Regards,
Alec Smecher
Public Knowledge Project Team