Upgrade fail/problems ojs 2.4.5 to 3.0.1

Hi @digitojs

Could you then get the OJS 3.0.2 code – either using the GitHub branch ojs-stable-3_0_2 or maybe we could first try with the 3.0.2 package downloaded from here: https://pkp.sfu.ca/ojs/ojs_download/ because this way is already familiar for you? Then do the same that you did for the 3.0.1 upgrade and report what messages do you see? Please keep the last 2.4.5 full backup (ojs, files, db), if something goes wrong and you should start the upgrade from new!
Let me know if you would need any help for this step…

Best,
Bozana

Thank you again bozana.

To keep the same line of action, let’s start by the package download and see how it goes.

First, when i restore the files_dir, it’s a folder from the last backup but where i added some files that where missing or at least that the upgrade process was complaining about. It was very time consuming to restore/create them each time i wanted to redo the upgade. So, i adjusted the folder and the error “cant find file”, “unable to find” or “skipping file” was gone. Same thing with folder scheduledTaskLogs, had to add it every time. You suggest i use this version or the “raw” from backup?

Thank you again,
Best regards

Hi @digitojs

Hmmm… OK, lets take then your corrected files_dir… (but please keep also the “raw” backup for some time)…

Best,
Bozana

After the first upgrade, it wasn’t successful.

  • New copy of package 3.0.2.
  • Changed owner of files, cache, public, config.inc to apache, the rest remain as after the unpacking, and permission to 777 (for testing purposes).
  • The files directory used was the one i had managed to avoid all the erros i’ve faced before.
  • GeoLiteCity.dat in plugins/generic/usageStats

Now, this is what i got:

upgrade.php

[code: Installer Installer::migrateFiles]

[code: Installer Installer::convertSupplementaryFiles]

Warning: copy(/home/files/journals/3//articles/1440/attachment/1440-1-3683-1-13-20121214.jpg): failed to open stream: No such file or directory in /var/www/html/ojs32/lib/pkp/classes/file/FileManager.inc.php on line 159

Warning: assert(): Assertion failed in /var/www/html/ojs32/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php on line 132

Warning: copy(/home/files/journals/3//articles/1440/attachment/1440-1-3686-1-13-20121214.jpg): failed to open stream: No such file or directory in /var/www/html/ojs32/lib/pkp/classes/file/FileManager.inc.php on line 159

Warning: assert(): Assertion failed in /var/www/html/ojs32/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php on line 132

Warning: copy(/home/files/journals/3//articles/1458/attachment/1458-1-3750-1-13-20130102.jpg): failed to open stream: No such file or directory in /var/www/html/ojs32/lib/pkp/classes/file/FileManager.inc.php on line 159

Warning: assert(): Assertion failed in /var/www/html/ojs32/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php on line 132

Warning: copy(/home/files/journals/3//articles/1458/attachment/1458-1-3754-1-13-20130102.jpg): failed to open stream: No such file or directory in /var/www/html/ojs32/lib/pkp/classes/file/FileManager.inc.php on line 159

(it goes on…)

Warning: copy(/home/files/journals/28//articles/3953/attachment/3953-1-15045-1-13-20170111.jpg): failed to open stream: No such file or directory in /var/www/html/ojs32/lib/pkp/classes/file/FileManager.inc.php on line 159

Warning: assert(): Assertion failed in /var/www/html/ojs32/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php on line 132

[code: Installer Installer::setFileUploader]

Fatal error: Call to a member function getId() on a non-object in /var/www/html/ojs32/classes/install/Upgrade.inc.php on line 930

  • these were exactly the kind of errors i had concerning files, and now its complaining about jpg files which extension was uppercase (.JPG) that i changed, and 2 pdf files that dont exist (i might have to the same as before and “create” them).

/var/log/php_errors.log

[23-Mar-2017 12:06:58 Europe/Lisbon] WARNING: Unable to find a match for “3953-15 044-1-SP.JPG” in “/home/files/journals/28//articles/3953/”. Skipping this file.
[23-Mar-2017 12:06:58 Europe/Lisbon] WARNING: Unable to find a match for “3953-15 045-1-SP.JPG” in “/home/files/journals/28//articles/3953/”. Skipping this file.
[23-Mar-2017 12:06:58 Europe/Lisbon] WARNING: Unable to find a match for “3752-14 104-1-SP.JPG” in “/home/files/journals/28//articles/3752/”. Skipping this file.
[23-Mar-2017 12:06:58 Europe/Lisbon] WARNING: Unable to find a match for “3752-14 105-1-SP.JPG” in “/home/files/journals/28//articles/3752/”. Skipping this file.
[23-Mar-2017 12:06:58 Europe/Lisbon] WARNING: Unable to find a match for “3752-14 106-1-SP.JPG” in “/home/files/journals/28//articles/3752/”. Skipping this file.
[23-Mar-2017 12:06:58 Europe/Lisbon] WARNING: Unable to find a match for “3752-14 107-1-SP.JPG” in “/home/files/journals/28//articles/3752/”. Skipping this file.
[23-Mar-2017 12:06:58 Europe/Lisbon] WARNING: Unable to find a match for “3752-14 108-1-SP.JPG” in “/home/files/journals/28//articles/3752/”. Skipping this file.
[23-Mar-2017 12:06:58 Europe/Lisbon] WARNING: Unable to find a match for “3752-14 109-1-SP.JPG” in “/home/files/journals/28//articles/3752/”. Skipping this file.
[23-Mar-2017 12:07:00 Europe/Lisbon] WARNING: Unable to find a match for “1410-35 69-2-SM.pdf” in “/home/files/journals/27//articles/1410/”. Skipping this file.
[23-Mar-2017 12:07:00 Europe/Lisbon] WARNING: Unable to find a match for “1699-64 95-1-LE.pdf” in “/home/files/journals/1//articles/1699/”. Skipping this file.

(it goes on with more jpg…)

[23-Mar-2017 12:07:12 Europe/Lisbon] PHP Warning: copy(/home/files/journals/3//a rticles/1440/attachment/1440-1-3683-1-13-20121214.jpg): failed to open stream: No such file or directory in /var/www/html/ojs32/lib/pkp/classes/file/FileManager.i nc.php on line 159
[23-Mar-2017 12:07:12 Europe/Lisbon] PHP Warning: assert(): Assertion failed in /var/www/html/ojs32/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php on line 132
[23-Mar-2017 12:07:12 Europe/Lisbon] PHP Warning: copy(/home/files/journals/3//a rticles/1440/attachment/1440-1-3686-1-13-20121214.jpg): failed to open stream: No such file or directory in /var/www/html/ojs32/lib/pkp/classes/file/FileManager.i nc.php on line 159
[23-Mar-2017 12:07:12 Europe/Lisbon] PHP Warning: assert(): Assertion failed in /var/www/html/ojs32/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php on line 132
[23-Mar-2017 12:07:14 Europe/Lisbon] PHP Warning: copy(/home/files/journals/3//a rticles/1458/attachment/1458-1-3750-1-13-20130102.jpg): failed to open stream: No such file or directory in /var/www/html/ojs32/lib/pkp/classes/file/FileManager.i nc.php on line 159
[23-Mar-2017 12:07:14 Europe/Lisbon] PHP Warning: assert(): Assertion failed in /var/www/html/ojs32/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php on line 132

(…)

[23-Mar-2017 12:07:43 Europe/Lisbon] PHP Fatal error: Call to a member function getId() on a non-object in /var/www/html/ojs32/classes/install/Upgrade.inc.php on line 930

/var/log/httpd/error_log

[Thu Mar 23 12:12:13 2017] [error] [client -ip] ojs2: 404 Not Found, referer: http://-ip/ojs32/
[Thu Mar 23 12:12:13 2017] [error] [client -ip] PHP Warning: require_once(/var/www/html/plugins/generic/alm/ArticleInfoSender.inc.php): failed to open stream: No such file or directory in /var/www/html/lib/pkp/includes/functions.inc.php on line 25, referer: http://-ip/ojs32/
[Thu Mar 23 12:12:13 2017] [error] [client -ip] PHP Fatal error: require_once(): Failed opening required ‘/var/www/html/plugins/generic/alm/ArticleInfoSender.inc.php’ (include_path=’.:/var/www/html/classes:/var/www/html/pages:/var/www/html/lib/pkp:/var/www/html/lib/pkp/classes:/var/www/html/lib/pkp/pages:/var/www/html/lib/pkp/lib/adodb:/var/www/html/lib/pkp/lib/phputf8:/var/www/html/lib/pkp/lib/pqp/classes:/var/www/html/lib/pkp/lib/smarty:.:/usr/share/pear:/usr/share/php’) in /var/www/html/lib/pkp/includes/functions.inc.php on line 25, referer: http://-ip/ojs32/
[Thu Mar 23 12:12:13 2017] [error] [client -ip] PHP Warning: require_once(/var/www/html/ojs32/plugins/generic/pln/classes/tasks/Depositor.inc.php): failed to open stream: No such file or directory in /var/www/html/ojs32/lib/pkp/includes/functions.inc.php on line 25
[Thu Mar 23 12:12:13 2017] [error] [client -ip] PHP Fatal error: require_once(): Failed opening required ‘/var/www/html/ojs32/plugins/generic/pln/classes/tasks/Depositor.inc.php’ (include_path=’.:/var/www/html/ojs32/classes:/var/www/html/ojs32/pages:/var/www/html/ojs32/lib/pkp:/var/www/html/ojs32/lib/pkp/classes:/var/www/html/ojs32/lib/pkp/pages:/var/www/html/ojs32/lib/pkp/lib/adodb:/var/www/html/ojs32/lib/pkp/lib/phputf8:/var/www/html/ojs32/lib/pkp/lib/pqp/classes:/var/www/html/ojs32/lib/pkp/lib/smarty:.:/usr/share/pear:/usr/share/php’) in /var/www/html/ojs32/lib/pkp/includes/functions.inc.php on line 25
[Thu Mar 23 12:12:37 2017] [error] [client -ip] ojs2: 404 Not Found
[Thu Mar 23 12:12:37 2017] [error] [client -ip] PHP Warning: require_once(/var/www/html/classes/tasks/ReviewReminder.inc.php): failed to open stream: No such file or directory in /var/www/html/lib/pkp/includes/functions.inc.php on line 25
[Thu Mar 23 12:12:37 2017] [error] [client -ip] PHP Fatal error: require_once(): Failed opening required ‘/var/www/html/classes/tasks/ReviewReminder.inc.php’ (include_path=’.:/var/www/html/classes:/var/www/html/pages:/var/www/html/lib/pkp:/var/www/html/lib/pkp/classes:/var/www/html/lib/pkp/pages:/var/www/html/lib/pkp/lib/adodb:/var/www/html/lib/pkp/lib/phputf8:/var/www/html/lib/pkp/lib/pqp/classes:/var/www/html/lib/pkp/lib/smarty:.:/usr/share/pear:/usr/share/php’) in /var/www/html/lib/pkp/includes/functions.inc.php on line 25

browser window

404 Not Found
Stack Trace:
File: /var/www/html/lib/pkp/classes/core/PKPPageRouter.inc.php line 203
Function: Dispatcher->handle404()

File: /var/www/html/lib/pkp/classes/core/Dispatcher.inc.php line 134
Function: PKPPageRouter->route(Object(Request))

File: /var/www/html/lib/pkp/classes/core/PKPApplication.inc.php line 227
Function: Dispatcher->dispatch(Object(Request))

File: /var/www/html/index.php line 68
Function: PKPApplication->execute()

Warning: require_once(/var/www/html/classes/tasks/ReviewReminder.inc.php): failed to open stream: No such file or directory in /var/www/html/lib/pkp/includes/functions.inc.php on line 25 Fatal error: require_once(): Failed opening required ‘/var/www/html/classes/tasks/ReviewReminder.inc.php’ (include_path=’.:/var/www/html/classes:/var/www/html/pages:/var/www/html/lib/pkp:/var/www/html/lib/pkp/classes:/var/www/html/lib/pkp/pages:/var/www/html/lib/pkp/lib/adodb:/var/www/html/lib/pkp/lib/phputf8:/var/www/html/lib/pkp/lib/pqp/classes:/var/www/html/lib/pkp/lib/smarty:.:/usr/share/pear:/usr/share/php’) in /var/www/html/lib/pkp/includes/functions.inc.php on line 25

What do you think? should i restore DB and files_dir with these errors fixed and try again?
Redo everything?

Thank you for your help!
Best regards

Hi @digitojs

Hmmm… Strange that all the images are missing :open_mouth: Do you maybe know what could happen to them, why are they missing? Could it be that you repaired the files_dir after the upgrade i.e. when it was already partly upgraded and not the “row” backup? Hmmm… Maybe to restore the “raw” backup (DB, files_dir, public_dir) and then try the upgrade again.
Also, it seems like no journal manager could be found. Is there a journal manager in that journal? Or could it be that you have some entries in the DB from another journal that does not exist any more?
Would it be maybe possible for you to give me your anonymized data, so that I can test it locally too?

Best,
Bozana

Just a small comment here: I had problems with files saved with uppercase file extensions while the script was searching for a lowercase file name, the fix I used is mentioned here: OJS 3.0 upgrade fails to move/rename some supplementary files - #6 by ajnyga (of course a backup is good to have before running anything). But: missing files did not affect the result of the upgrade in our case.

I think that those uper-/lower-case issue for file names is solved in OJS 3.0.2 with this PR: pkp/pkp-lib#1924 fix file names upgrade and supp file array by bozana · Pull Request #1203 · pkp/ojs · GitHub
But it could be that @digitojs had that problem when first upgrading to 3.0.1…
So maybe also that’s why the “raw” backup should be used…

Thank you both for your replies, @bozana and @ajnyga.

About the files directory: in previous upgrades to 3.0.1, i used the files_dir extracted from the backup that has the files, ojs, and db. With all the errors that it was throwing about mismatching and whatever, i “created” the files (copied and renamed to the expected name) that it was complaining were missing and i also renamed the .JPG to .jpg, that were giving problems. All those errors were gone.

I tried this so many times, and to make the test and restore faster, i extracted the files_dir from the same backup package used to extract the db to dump. So, files and DB are from the same day.

The files_dir i used from that point (and in this 3.0.2 test too), is the original one only with the renamed .JPG files and the .pdfs and .txt i added to make it past the “missing” errors. Which is interesting because now it complains about the .jpg that were giving “uppercase error” in 3.0.1, and two .pdf files that were not a problem before (i checked and they dont exist in the original backup files_dir).

Each time i try this, i delete files_dir and DB, then i restore the DB from that .sql and use this files_dir that has some errors fixed. Both are on the server, so i just copy and dump them.

I will try now with the original-not fixed files_dir, and the public files that i forgot to copy last time to the public of 3.0.2.

About the journal manager, i will look for it after trying this again!

Thank you.
Best regards

@bozana

I appreciate the help and i can give you the data you need for testing, just ask for what is needed.

Thank you.

Hello,

Test performed.
files_dir and DB restored from backup, public_dir copied from previous 2.4.5.

upgrade.php

[code: Installer Installer::convertSupplementaryFiles]

Warning: copy(/home/files/journals/20//articles/450/attachment/450-1-1506-1-13-20120125.doc): failed to open stream: No such file or directory in /var/www/html/ojs32/lib/pkp/classes/file/FileManager.inc.php on line 159

Warning: assert(): Assertion failed in /var/www/html/ojs32/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php on line 132

Warning: copy(/home/files/journals/3//articles/1730/attachment/1730-1-5003-2-13-20140116.jpg): failed to open stream: No such file or directory in /var/www/html/ojs32/lib/pkp/classes/file/FileManager.inc.php on line 159

Warning: assert(): Assertion failed in /var/www/html/ojs32/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php on line 132

[code: Installer Installer::setFileUploader]

Fatal error: Call to a member function getId() on a non-object in /var/www/html/ojs32/classes/install/Upgrade.inc.php on line 930

only these lines are reported!

/var/log/php_errors.log

[23-Mar-2017 16:27:43 Europe/Lisbon] WARNING: Unable to find a match for “1410-3569-2-SM.pdf” in “/home/files/journals/27//articles/1410/”. Skipping this file.
[23-Mar-2017 16:27:43 Europe/Lisbon] WARNING: Unable to find a match for “1410-3570-1-RV.pdf” in “/home/files/journals/27//articles/1410/”. Skipping this file.
[23-Mar-2017 16:27:43 Europe/Lisbon] WARNING: Unable to find a match for “1699-6495-1-LE.pdf” in “/home/files/journals/1//articles/1699/”. Skipping this file.
[23-Mar-2017 16:27:45 Europe/Lisbon] WARNING: Unable to find a match for “1730-5002-1-SM.docx” in “/home/files/journals/3//articles/1730/”. Skipping this file.
[23-Mar-2017 16:27:45 Europe/Lisbon] WARNING: Unable to find a match for “1730-5004-1-RV.docx” in “/home/files/journals/3//articles/1730/”. Skipping this file.
[23-Mar-2017 16:27:45 Europe/Lisbon] WARNING: Unable to find a match for “1730-5003-2-SP.jpg” in “/home/files/journals/3//articles/1730/”. Skipping this file.
[23-Mar-2017 16:27:47 Europe/Lisbon] WARNING: Unable to find a match for “450-1506-1-SP.doc” in “/home/files/journals/20//articles/450/”. Skipping this file.
[23-Mar-2017 16:27:48 Europe/Lisbon] WARNING: Unable to find a match for “3385-12660-1-SM.pdf” in “/home/files/journals/38//articles/3385/”. Skipping this file.
[23-Mar-2017 16:27:48 Europe/Lisbon] WARNING: Unable to find a match for “3385-12661-1-RV.pdf” in “/home/files/journals/38//articles/3385/”. Skipping this file.
[23-Mar-2017 16:27:48 Europe/Lisbon] WARNING: Unable to find a match for “3385-12662-1-CE.pdf” in “/home/files/journals/38//articles/3385/”. Skipping this file.
[23-Mar-2017 16:27:49 Europe/Lisbon] WARNING: Unable to find a match for “2075-6679-1-SM.pdf” in “/home/files/journals/6//articles/2075/”. Skipping this file.
[23-Mar-2017 16:27:49 Europe/Lisbon] WARNING: Unable to find a match for “2075-6680-1-RV.pdf” in “/home/files/journals/6//articles/2075/”. Skipping this file.
[23-Mar-2017 16:27:49 Europe/Lisbon] WARNING: Unable to find a match for “2075-6681-1-CE.pdf” in “/home/files/journals/6//articles/2075/”. Skipping this file.
[23-Mar-2017 16:27:49 Europe/Lisbon] WARNING: Unable to find a match for “2075-6682-1-PB.pdf” in “/home/files/journals/6//articles/2075/”. Skipping this file.
[23-Mar-2017 16:27:49 Europe/Lisbon] WARNING: Unable to find a match for “3908-14823-1-SM.pdf” in “/home/files/journals/6//articles/3908/”. Skipping this file.
[23-Mar-2017 16:27:49 Europe/Lisbon] WARNING: Unable to find a match for “3908-14824-1-RV.pdf” in “/home/files/journals/6//articles/3908/”. Skipping this file.
[23-Mar-2017 16:27:49 Europe/Lisbon] WARNING: Unable to find a match for “3908-14825-1-CE.pdf” in “/home/files/journals/6//articles/3908/”. Skipping this file.
[23-Mar-2017 16:27:50 Europe/Lisbon] WARNING: Unable to find a match for “1710-4917-1-SM.docx” in “/home/files/journals/8//articles/1710/”. Skipping this file.
[23-Mar-2017 16:27:50 Europe/Lisbon] WARNING: Unable to find a match for “1710-4921-1-RV.docx” in “/home/files/journals/8//articles/1710/”. Skipping this file.
[23-Mar-2017 16:27:51 Europe/Lisbon] WARNING: Unable to find a match for “2570-8789-1-SM.pdf” in “/home/files/journals/8//articles/2570/”. Skipping this file.
[23-Mar-2017 16:27:51 Europe/Lisbon] WARNING: Unable to find a match for “2570-8791-1-RV.pdf” in “/home/files/journals/8//articles/2570/”. Skipping this file.
[23-Mar-2017 16:27:51 Europe/Lisbon] WARNING: Unable to find a match for “2570-8792-1-CE.pdf” in “/home/files/journals/8//articles/2570/”. Skipping this file.
[23-Mar-2017 16:27:51 Europe/Lisbon] WARNING: Unable to find a match for “2570-8793-1-PB.pdf” in “/home/files/journals/8//articles/2570/”. Skipping this file.
[23-Mar-2017 16:27:53 Europe/Lisbon] PHP Warning: copy(/home/files/journals/20//articles/450/attachment/450-1-1506-1-13-20120125.doc): failed to open stream: No such file or directory in /var/www/html/ojs32/lib/pkp/classes/file/FileManager.inc.php on line 159
[23-Mar-2017 16:27:53 Europe/Lisbon] PHP Warning: assert(): Assertion failed in /var/www/html/ojs32/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php on line 132
[23-Mar-2017 16:28:02 Europe/Lisbon] PHP Warning: copy(/home/files/journals/3//articles/1730/attachment/1730-1-5003-2-13-20140116.jpg): failed to open stream: No such file or directory in /var/www/html/ojs32/lib/pkp/classes/file/FileManager.inc.php on line 159
[23-Mar-2017 16:28:02 Europe/Lisbon] PHP Warning: assert(): Assertion failed in /var/www/html/ojs32/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php on line 132
[23-Mar-2017 16:28:26 Europe/Lisbon] PHP Fatal error: Call to a member function getId() on a non-object in /var/www/html/ojs32/classes/install/Upgrade.inc.php on line 930

when i access …/ojs2/phpmyadmin:

404 Not Found
Stack Trace:
File: /var/www/html/lib/pkp/classes/core/PKPPageRouter.inc.php line 203
Function: Dispatcher->handle404()

File: /var/www/html/lib/pkp/classes/core/Dispatcher.inc.php line 134
Function: PKPPageRouter->route(Object(Request))

File: /var/www/html/lib/pkp/classes/core/PKPApplication.inc.php line 227
Function: Dispatcher->dispatch(Object(Request))

File: /var/www/html/index.php line 68
Function: PKPApplication->execute()

Warning: in_array() expects parameter 2 to be array, null given in /var/www/html/lib/pkp/plugins/generic/usageStats/PKPUsageStatsLoader.inc.php on line 195 Warning: in_array() expects parameter 2 to be array, null given in /var/www/html/lib/pkp/plugins/generic/usageStats/PKPUsageStatsLoader.inc.php on line 196 Warning: in_array() expects parameter 2 to be array, null given in /var/www/html/lib/pkp/plugins/generic/usageStats/PKPUsageStatsLoader.inc.php on line 195 Warning: in_array() expects parameter 2 to be array, null given in /var/www/html/lib/pkp/plugins/generic/usageStats/PKPUsageStatsLoader.inc.php on line 196 Warning: in_array() expects parameter 2 to be array, null given in /var/www/html/lib/pkp/plugins/generic/usageStats/PKPUsageStatsLoader.inc.php on line 195 Warning: in_array() expects parameter 2 to be array, null given in /var/www/html/lib/pkp/plugins/generic/usageStats/PKPUsageStatsLoader.inc.php on line 196 Warning: in_array() expects parameter 2 to be array, null given in /var/www/html/lib/pkp/plugins/generic/usageStats/PKPUsageStatsLoader.inc.php on line 195 Warning: in_array() expects parameter 2 to be array, null given in /var/www/html/lib/pkp/plugins/generic/usageStats/PKPUsageStatsLoader.inc.php on line 196 Warning: in_array() expects parameter 2 to be array, null given in /var/www/html/lib/pkp/plugins/generic/usageStats/PKPUsageStatsLoader.inc.php on line 195

/var/log/httpd/error_log

[Thu Mar 23 16:34:11 2017] [error] [client -ip] PHP Warning: in_array() expects parameter 2 to be array, null given in /var/www/html/lib/pkp/plugins/generic/usageStats/PKPUsageStatsLoader.inc.php on line 195
[Thu Mar 23 16:34:11 2017] [error] [client -ip] PHP Warning: in_array() expects parameter 2 to be array, null given in /var/www/html/lib/pkp/plugins/generic/usageStats/PKPUsageStatsLoader.inc.php on line 196
[Thu Mar 23 16:34:11 2017] [error] [client -ip] PHP Warning: require_once(/var/www/html/plugins/generic/alm/ArticleInfoSender.inc.php): failed to open stream: No such file or directory in /var/www/html/lib/pkp/includes/functions.inc.php on line 25
[Thu Mar 23 16:34:11 2017] [error] [client -ip] PHP Fatal error: require_once(): Failed opening required ‘/var/www/html/plugins/generic/alm/ArticleInfoSender.inc.php’ (include_path=’.:/var/www/html/classes:/var/www/html/pages:/var/www/html/lib/pkp:/var/www/html/lib/pkp/classes:/var/www/html/lib/pkp/pages:/var/www/html/lib/pkp/lib/adodb:/var/www/html/lib/pkp/lib/phputf8:/var/www/html/lib/pkp/lib/pqp/classes:/var/www/html/lib/pkp/lib/smarty:.:/usr/share/pear:/usr/share/php’) in /var/www/html/lib/pkp/includes/functions.inc.php on line 25

So, basically same output…

Thank you in advance,
Best regards

Hello @bozana,

i’ve checked the journal manager issue. From what i could understand, there’s some problem with journal number “3”, which i think was the one you were mentioning… i cant see the roles or pretty much anything useful besides there are active articles.

Hope it helps something.

Thank you!

Hi @digitojs

Is that journal no. 3 an active, existing journal? – If it has no roles and users, it looks like it is not…
Do those missing files (e.g. 1410-3569-2-SM.pdf) maybe have that journal_id?

Thanks!
Bozana

Hello @bozana,

I consulted ojs administrators and it seems that journal (3) is not active. It has to be there, but there is no actual activity, the editorial process is aside from ojs.
The missing files are refering to several journals…27, 1, 6, 3, 38, 8, 20. What can we do?

Thank you for your help!
Best regards

Hi @digitojs

Could you then check if each journal has a journal manager and if not to create one?
Do you know if those files are really missing or something else is the problem, e.g. if they exist but within a different folder or the file ending is different or … ?
Could you maybe send me your “raw” files_dir and anonymized “raw” DB dump? Maybe via e-mail: bozana dot bokan at posteo dot net. Or, if too big, somehow differently…

Best,
Bozana

Hello @bozana,

I’ll check the journals for the journals managers, but i’ll have to restore the previous 2.4.5 version to look for it and, possibly, create the roles.
The files are missing, it’s similar to what happened before and what i did to correct it was to copy a file with a similar name and rename it. Except the images, those weren’t missing, only the uppercase issue.

I can send you the files, but my files_dir has almost 20GB so i don’t know what could be the best way. DB dump is 120mb. I’ll email you.

Thank you!
Best regards

Hello @bozana,

how should i do to create the anonymized db dump? The best way to fit your needs.

Thank you,
Best regards

Hi @digitojs

At least set the columns username, password, first_name, last_name, email in the table users to some anonym values. They could all have the same values. Also remove entries in the columns phone, fax, mailing_address, billing_address.

Best,
Bozana

Hello,

I’ve checked all the journals and files.
About the missing files: the ones from the last performed test, are all missing. From single files like jpg and pdf, to article folders as a whole, like /journals/8//articles/2570/ or /journals/6//articles/2075/, and as a consequence all the files it reports are missing and should be inside. I have no explanation for this, they don’t existe in my files_dir.

As for the journal managers, i’ve checked all these journal_ids and the journals exist. And they all have roles and users, they all have journal managers, including my admin user (only for journal_id 3 my admin user was not a journal manager, and i add it).

My 2.4.5 version runs fine, i had no problems restoring it, so what should i do? If i try the upgrade i’ll get the same issues for sure.

Thank you,
Best regards

Hi @digitojs

I am afraid that you will then have to restore that missing files :frowning: They should be restored in the “raw” files_dir in the appropriate subfolder – maybe then check via GUI that they work fine.

I see you are using ALM plugin, right? I am not sure it works with OJS 3.x, so maybe to remove that for now. Is there maybe any other plugin that you are using but it is not within the release?

Best,
Bozana

Hello @bozana,

I’ll restore the files to test it again.
Did you receive my email with the DB?
The plugins that it complains in previous logs are ALM, PLN and usagestats. I didn’t find information about them in the release docs, do you know if they are problematic? I’ll have to disable them journal by journal?

Thank you!
Best regards,