Just thinking that you already hit the max signed value of INT (2147483647) with 3135031360 and unsigned max is close (4294967295). Well not actually close if you do not get thousands of submissions daily. The transfer plugin will reset all those value, because it is designed to work in a situation where you transfer a journal to another installation that has for example matching submission id’s.
Yeah, I do not get that many submissions. It’s a small(ish) journal. We will see tomorrow if this upgrade fails again.
Yet another failure but this time on a different php file… so no debug detail there. Need to add some more
(mysql): SELECT s.*, ps.date_published,
COALESCE(stl.setting_value, stpl.setting_value) AS section_title,
COALESCE(sal.setting_value, sapl.setting_value) AS section_abbrev
FROM submissions s
LEFT JOIN published_submissions ps ON (s.submission_id = ps.submission_id)
JOIN sections se ON se.section_id = s.section_id
LEFT JOIN section_settings stpl ON (se.section_id = stpl.section_id AND stpl.setting_name = 'title' AND stpl.locale = 'pt_BR')
LEFT JOIN section_settings stl ON (se.section_id = stl.section_id AND stl.setting_name = 'title' AND stl.locale = 'pt_BR')
LEFT JOIN section_settings sapl ON (se.section_id = sapl.section_id AND sapl.setting_name = 'abbrev' AND sapl.locale = 'pt_BR')
LEFT JOIN section_settings sal ON (se.section_id = sal.section_id AND sal.setting_name = 'abbrev' AND sal.locale = 'pt_BR')
WHERE s.submission_id = 34188
----<hr>
PHP Fatal error: Call to a member function getContextId() on null in /var/www/ojs/lib/pkp/classes/submission/reviewAssignment/ReviewAssignment.inc.php on line 526
-----<hr>But you are trough the setFileName section 
I would still at least consider using the fulljournaltransfer to move the installation before upgrading.
This will of course change the submission id’s and therefore also article url’s which is a drawback. But having large table id’s like you have now does not sound too good either. At least find out what does it mean for performance that the value is unsigned. I am pretty sure that the high numbers there have cause the upgrade to take long.
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Export worked fine, but import failed.
Here is the log of the import plugin.
root@server3273:/var/www/projetos/buscalegis/revistas# php tools/importExport.php FullJournalImportExportPlugin import revistasexport.tar.gz
ojs2 has produced an error
Message: WARNING: copy(/var/www/ojsfiles_novo/fullJournalImportExport/files/articles/31350/public/31350-35163-10-PB.html): failed to open stream: No such file or directory
In file: /var/www/ojslib/pkp/classes/file/FileManager.inc.php
At line: 152
Stacktrace:
Server info:
OS: Linux
PHP Version: 5.6.37-1+ubuntu16.04.1+deb.sury.org+1
Apache Version: N/A
DB Driver: mysql
DB server version: 5.7.23-0ubuntu0.16.04.1
ojs2 has produced an error
Message: WARNING: unlink(/var/www/ojsfiles_novo/fullJournalImportExport/files/articles/31350/public/31350-35163-10-PB.html): No such file or directory
In file: /var/www/ojsplugins/importexport/fullJournalTransfer/XMLDisassembler.inc.php
At line: 666
Stacktrace:
Server info:
OS: Linux
PHP Version: 5.6.37-1+ubuntu16.04.1+deb.sury.org+1
Apache Version: N/A
DB Driver: mysql
DB server version: 5.7.23-0ubuntu0.16.04.1
<h1>DB Error: Incorrect date value: '&nbsp;' for column 'date_created' at row 1</h1>ojs2: DB Error: Incorrect date value: ' ' for column 'date_created' at row 1
It talks about files missing in the damn 31350, but it’s not the actual error.
Incorrect date value: ' ' for column 'date_created' at row 1
Not sure where this is failing though, will search the DB for anything like that
I’m checking all Tables that have the " date_created" column to see if I can find out where is that being inserted from, but I found something else in the meanwhile
select * from objects_for_review
mysql> select * from notifications ;
+-----------------+------------+---------+-------+-----------+---------------------+-----------+------------+----------+
| notification_id | context_id | user_id | level | type | date_created | date_read | assoc_type | assoc_id |
+-----------------+------------+---------+-------+-----------+---------------------+-----------+------------+----------+
| 1 | 3 | 50 | 2 | 16777233 | 2011-08-18 18:30:09 | NULL | 257 | 34076 |
| 2 | 3 | 90 | 2 | 16777233 | 2011-08-18 18:30:09 | NULL | 257 | 34076 |
| 3 | 3 | 13 | 2 | 16777233 | 2011-08-18 18:30:09 | NULL | 257 | 34076 |
| 4 | 3 | 910 | 2 | 16777233 | 2011-08-18 18:30:09 | NULL | 257 | 34076 |
| 5 | 3 | 802 | 2 | 16777233 | 2011-08-18 18:30:09 | NULL | 257 | 34076 |
| 6 | 3 | 50 | 2 | 16777233 | 2011-08-18 18:30:55 | NULL | 257 | 34076 |
| 7 | 3 | 90 | 2 | 16777233 | 2011-08-18 18:30:55 | NULL | 257 | 34076 |
| 8 | 3 | 13 | 2 | 16777233 | 2011-08-18 18:30:55 | NULL | 257 | 34076 |
| 9 | 3 | 910 | 2 | 16777233 | 2011-08-18 18:30:55 | NULL | 257 | 34076 |
| 10 | 3 | 802 | 2 | 16777233 | 2011-08-18 18:30:55 | NULL | 257 | 34076 |
| 11 | 3 | 1122 | 2 | 16777233 | 2011-08-18 19:27:28 | NULL | 257 | 34078 |
| 12 | 3 | 90 | 2 | 16777233 | 2011-08-18 19:27:28 | NULL | 257 | 34078 |
| 13 | 3 | 6 | 2 | 16777233 | 2011-08-18 19:27:28 | NULL | 257 | 34078 |
| 14 | 3 | 13 | 2 | 16777233 | 2011-08-18 19:27:28 | NULL | 257 | 34078 |
| 15 | 3 | 6 | 2 | 16777233 | 2011-08-18 19:27:28 | NULL | 257 | 34078 |
| 16 | 3 | 908 | 2 | 16777233 | 2011-08-18 19:27:28 | NULL | 257 | 34078 |
| 17 | 3 | 4 | 2 | 16777233 | 2011-08-18 19:27:28 | NULL | 257 | 34078 |
| 18 | 3 | 13 | 2 | 16777233 | 2011-08-18 19:27:28 | NULL | 257 | 34078 |
| 19 | 3 | 1121 | 2 | 16777234 | 2011-08-18 20:19:25 | NULL | 257 | 34084 |
| 20 | 3 | 6 | 2 | 16777234 | 2011-08-18 20:19:25 | NULL | 257 | 34084 |
| 21 | 3 | 13 | 2 | 16777234 | 2011-08-18 20:19:25 | NULL | 257 | 34084 |
| 22 | 3 | 1132 | 2 | 16777234 | 2011-08-18 20:19:25 | NULL | 257 | 34084 |
| 23 | 3 | 22 | 2 | 16777234 | 2011-08-18 20:19:25 | NULL | 257 | 34084 |
| 24 | 3 | 13 | 2 | 16777234 | 2011-08-18 20:19:25 | NULL | 257 | 34084 |
| 25 | 3 | 1 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 26 | 3 | 2 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 27 | 3 | 3 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 28 | 3 | 4 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 29 | 3 | 5 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 30 | 3 | 6 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 31 | 3 | 7 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 32 | 3 | 13 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 33 | 3 | 17 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 34 | 3 | 18 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 35 | 3 | 22 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 36 | 3 | 24 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 37 | 3 | 25 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 38 | 3 | 50 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 39 | 3 | 90 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 40 | 3 | 109 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 41 | 3 | 125 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 42 | 3 | 228 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 43 | 3 | 278 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 44 | 3 | 310 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 45 | 3 | 358 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 46 | 3 | 369 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 47 | 3 | 370 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 48 | 3 | 372 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 49 | 3 | 414 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 50 | 3 | 429 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 51 | 3 | 433 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 52 | 3 | 443 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 53 | 3 | 444 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 54 | 3 | 445 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 55 | 3 | 473 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 56 | 3 | 482 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 57 | 3 | 496 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 58 | 3 | 511 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
| 59 | 3 | 547 | 2 | 268435478 | 2011-08-18 20:27:16 | NULL | 0 | 0 |
See those all with seconds from each other? That has to be SPAM submission somehow. Is there anything I could try to identify those? there are 26k there: those cannot be all real. .
the object_for_review is a plugin related table. The plugin (objects for review) has not been ported to OJS3 yet.
Yep, just found that out…
Not sure if this is causing issues or not really, the export plugin should be able to handle those situations.
But most likely I can truncate that table without too much damage, what do you think?
If you have not used the plugin? Maybe a good idea to create a dump first if you have used it and it is ported to OJS3 later.
At this point, I would be glad to just be able to get a semi functional copy of the original one (which had issues anyway).
ARG, that was a mistake. the table is actually
notifications
there the close timestamps make sense.
did you check the xml file that was exported. maybe you can fix the date field by editing that file with vim?
It could just be that the same problems that cause problems with the upgrade mess up the export file…
In the process of slowly downloading the export to my machine. In the meanwhile, I’m trying another export with the truncate table
Hey! It worked! I was able to export and import , finally. I had to manually find the dates with ‘nbsp’ and change to a real date/time.
I’ve then started to upgrade to 3 and it finally worked!!!
@ajnyga Thank you so much for your tremendous effort to help me.
Anyone else that comes in this thread: Much of the issues I’ve faced here are not related to the initial error
PHP Fatal error: Call to a member function getStatus() on null in /dir/where/ojs/is/installed/classes/install/Upgrade.inc.php on line 1369
That particular issue was resolved when we figured out where the nulls where in the database (articles with null in section_id) for me.
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Last issue for now is that I’m seeing some items like that below:
This ##user.reviwerPrompt.optin## instead of the actual text.
Those are missing translations. What locale is that?
That’s pt_BR. Weird that there are missing translation. But at least it is not a DB issue anymore ¯\_(ツ)_/¯
those keys are a very recent addition. I think from June.
btw. did you check if the transferplugin solved the issue with very large file id’s?
Nope, I need to double check that. But I’ve also deleted 3 journals that were not required anymore and those high numbers where in those journals, so they were not transferred at all. But I need to check if the DB is in good shape.
the auto increment value is probably the thing to check then. Especially in the submission files table where id was very high. As I said, not sure if the unsigned value is a problem though.