After upgrading to OJS 3.1.1.4 files are not found

Hello dear @asmecher,

I have upgraded, again OJS 2.4 to 3.1.1.4 but I got the same results. The Apache error is as next:

[Wed Oct 03 14:42:11.164867 2018] [:error] [pid 860:tid 2032] [client ::1:55182] WARNING: Unable to find a match for “1266-3444-1-RV.pdf” in “C:/xampp2/htdocs/myojs/files/journals/7//articles/1266/”. Skipping this file., referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:55.627539 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:55.631555 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:55.635541 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:55.659538 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:55.685855 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:55.721524 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:55.749525 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:55.793524 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:55.834908 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:55.878908 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:55.924241 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:55.970279 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:56.018248 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:56.054272 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:56.102247 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:56.148167 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:56.215020 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:56.268799 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:56.312832 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:56.368839 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:57.666689 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:58.022689 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:58.022689 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:58.513685 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:42:58.513685 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:44:04.742745 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:44:04.746746 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:45:11.256281 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:45:25.591349 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:45:25.595348 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:45:25.985243 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:45:54.656243 2018] [:error] [pid 860:tid 2032] [client ::1:55182] WARNING: Unable to find a match for “1485-4335-1-SM.phtml” in “C:/xampp2/htdocs/myojs/files/journals/1//articles/1485/”. Skipping this file., referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:46:05.664793 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:46:05.698578 2018] [:error] [pid 860:tid 2032] [client ::1:55182] WARNING: Unable to find a match for “1266-3442-1-SM.pdf” in “C:/xampp2/htdocs/myojs/files/journals/7//articles/1266/”. Skipping this file., referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:46:05.698578 2018] [:error] [pid 860:tid 2032] [client ::1:55182] WARNING: Unable to find a match for “1266-3445-1-PB.pdf” in “C:/xampp2/htdocs/myojs/files/journals/7//articles/1266/”. Skipping this file., referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:46:05.776522 2018] [:error] [pid 860:tid 2032] [client ::1:55182] WARNING: Unable to find a match for “1359-3801-1-PB.pdf” in “C:/xampp2/htdocs/myojs/files/journals/7//articles/1359/”. Skipping this file., referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:46:24.591634 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:46:24.944312 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:46:26.000938 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:46:28.503390 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:46:29.631072 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:46:30.582216 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:46:31.448652 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:46:34.274237 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:47:53.144865 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Notice: unserialize(): Error at offset 3888 of 65535 bytes in C:\xampp2\htdocs\myojs\lib\pkp\classes\db\DAO.inc.php on line 352, referer: http://localhost/myojs/index.php/index/install/upgrade
[Wed Oct 03 14:47:58.983578 2018] [:error] [pid 860:tid 2032] [client ::1:55182] PHP Warning: Element ‘<ahref|target><em><strong><cite><code><ul><ol><li><dl><dt><dd><b><i><u><imgsrc|alt><sup><sub><br><p>’ is not supported (for information on implementing this, see the support forums) in C:\xampp2\htdocs\myojs\lib\pkp\lib\vendor\ezyang\htmlpurifier\library\HTMLPurifier\HTMLDefinition.php on line 311, referer: http://localhost/myojs/index.php/index/install/upgrade

best regards,
Juan Pablo

Hi @asmecher,

The permissions looks like:

giron@LAPTOP-NLJPA8IC MINGW64 /c/xampp2/htdocs/myojs
$ ls -al
total 113
drwxr-xr-x 1 giron 197609 0 Oct 3 14:32 ./
drwxr-xr-x 1 giron 197609 0 Oct 2 11:46 …/
drwxr-xr-x 1 giron 197609 0 Oct 3 14:30 api/
drwxr-xr-x 1 giron 197609 0 Oct 3 14:51 cache/
drwxr-xr-x 1 giron 197609 0 Oct 3 14:30 classes/
-rw-r–r-- 1 giron 197609 16870 Oct 3 14:51 config.inc.php
drwxr-xr-x 1 giron 197609 0 Oct 3 14:30 controllers/
drwxr-xr-x 1 giron 197609 0 Oct 3 14:30 dbscripts/
drwxr-xr-x 1 giron 197609 0 Oct 3 14:30 docs/
-rw-r–r-- 1 giron 197609 1150 Sep 11 12:47 favicon.ico
drwxr-xr-x 1 giron 197609 0 Oct 3 14:51 files/
-rw-r–r-- 1 giron 197609 2973 Sep 11 12:47 index.php
drwxr-xr-x 1 giron 197609 0 Oct 3 14:30 js/
drwxr-xr-x 1 giron 197609 0 Oct 3 14:30 lib/
drwxr-xr-x 1 giron 197609 0 Oct 3 14:31 locale/
drwxr-xr-x 1 giron 197609 0 Oct 3 14:31 pages/
drwxr-xr-x 1 giron 197609 0 Oct 3 14:32 plugins/
drwxr-xr-x 1 giron 197609 0 Oct 3 14:32 public/
-rw-r–r-- 1 giron 197609 2445 Sep 11 12:47 README.md
drwxr-xr-x 1 giron 197609 0 Oct 3 14:32 registry/
-rw-r–r-- 1 giron 197609 32 Sep 11 12:47 robots.txt
drwxr-xr-x 1 giron 197609 0 Oct 3 14:32 styles/
drwxr-xr-x 1 giron 197609 0 Oct 3 14:32 templates/
drwxr-xr-x 1 giron 197609 0 Oct 3 14:32 tools/

Hi @Juan_Pablo_Giron_Rui,

There seem to be several things happening here:

  • Beware that your files_dir (configured in config.inc.php, and apparently files in your case) might be putting you at risk. See the “Recommended Configuration” area of docs/README.
  • The unserialize warnings might be caused by an accidental change of localization settings. Make sure your character set / localization settings are the same in your OJS 3.x config.inc.php as they were in your OJS 2.x config.inc.php file.
  • If you get just a few missing file warnings, it’s possible that these files are simply missing. If you get many, however, I’d suggest looking into why the files aren’t there. If you’re running an upgrade on an installation that already had an upgrade partially run on it, some of these files may already have been renamed. Be sure to restore everything from backup after an upgrade fails, including the files directory, to make sure the next run completes successfully.

Regards,
Alec Smecher
Public Knowledge Project Team

Hello @asmecher,

I moved the files folder from position, but the problem persist. I verified that localization and charset in my previous OJS 2.3 and it is the same in OJS 3.1.1.4 (config.ini.php). I don’t know how I could fix this issue. I have made the upgrading by three times, but unfortunately the error seems in some algorithm but I don’t know which.

Let me tell you a brief history about my upgrading process from OJS 2.3.7 to 3.1.1.4, may be it be useful to resolve this issue.

Initially, my database was in postgresql, I tried to upgrade my old OJS 2.3 to OJS 2.4 (acting as bridge to upgrade after to OJS 3.x). Unfortunately I had many issues then I decided migrating to MySQL. In database migration process, I had some issues with the original data such as: In articles table, 73 articles were without section_id, as there papers were from 2012 then I decided set the section id equal to 1. The second issue that I found was with the review_rounds table where the index must be UNIQUE but one column that was part of this index had value NULL, then in the upgrading process it failed. I decided remove the duplicates (I don’t know if it was the guilty). After these modification to original database I got to do the migration in databases with successfully. With the database in MySQL the migration from OJS 2.3 to 2.4 (Here I can see my papers) and 2.4. to 3.1 (I can’t see my papers) was relatively fast and simple.

I hope that previous history can help us to understand the problem.

thank you so much.

PD: config.ini.php

locale = es_ES
connection_charset = utf8
database_charset = utf8
charset_normalization = Off

files_dir = “C:/xampp2/submission_files”
public_files_dir = public

my tree project:

xammp2
----files
----htdocs
--------myojs
------------public

thks so much!

Hi @Juan_Pablo_Giron_Rui,

What do you have in C:/xampp2/submission_files? Can you show a few examples of file paths/names?

Regards,
Alec Smecher
Public Knowledge Project Team

Hello @asmecher, sure I attached some figures with the current submission_files directory.

path: C:\xampp2\submission_files

image

path: C:\xampp2\submission_files\journals

image

path: C:\xampp2\submission_files\journals\1

image

path: C:\xampp2\submission_files\journals\1\articles

image

path: C:\xampp2\submission_files\journals\1\articles\1

image

path: C:\xampp2\submission_files\journals\1\articles\1\public

image

I hope those screenshots can help.

regards,
Juan Pablo

Hi @Juan_Pablo_Giron_Rui,

At least one of the listed files is a virus. As long as your files directory is outside the web root or protected from direct access by .htaccess or similar, uploads like these are harmless – but beware that someone may have already leveraged one if your files directory was previously unsafely deployed.

The filenames for your submission files are still OJS 2.x style filenames. The upgrade should have renamed these. Did you get any warnings during the upgrade process?

Regards,
Alec Smecher
Public Knowledge Project Team

Hi @asmecher,

I tried to repeat the migration process on ubuntu, but unfurtunately I get upgrade from OJS 2.3 to OJS 2.4 but when I tried to migrate to OJS 3.1. I get 404 File Not Found. Really, I don’t know what is the problem. I got the follow log from Apache error.log file.

[Tue Oct 16 20:53:37.435282 2018] [:error] [pid 20735] [client 127.0.0.1:58958] WARNING: Unable to find a match for “1699-4980-1-RV.phtml” in “/var/www/submission_files/journals/1//articles/1699/”. Skipping this file., referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 21:03:33.408187 2018] [:error] [pid 20735] [client 127.0.0.1:58958] WARNING: Unable to find a match for “1485-4335-1-SM.phtml” in “/var/www/submission_files/journals/1//articles/1485/”. Skipping this file., referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 21:03:34.227544 2018] [:error] [pid 20735] [client 127.0.0.1:58958] WARNING: Unable to find a match for “1693-4954-1-SM.phtml” in “/var/www/submission_files/journals/1//articles/1693/”. Skipping this file., referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 21:03:34.243627 2018] [:error] [pid 20735] [client 127.0.0.1:58958] WARNING: Unable to find a match for “1699-4979-1-SM.phtml” in “/var/www/submission_files/journals/1//articles/1699/”. Skipping this file., referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 21:03:34.248131 2018] [:error] [pid 20735] [client 127.0.0.1:58958] WARNING: Unable to find a match for “1700-4981-1-SM.phtml” in “/var/www/submission_files/journals/1//articles/1700/”. Skipping this file., referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 21:03:34.479467 2018] [:error] [pid 20735] [client 127.0.0.1:58958] WARNING: Unable to find a match for “1721-5060-1-SM.phtml” in “/var/www/submission_files/journals/1//articles/1721/”. Skipping this file., referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 21:07:00.090647 2018] [:error] [pid 20735] [client 127.0.0.1:58958] PHP Warning: Element ‘<a><em><strong><cite><code><ul><ol><li><dl><dt><dd><b><i><u><imgsrc|alt><sup><sub><br><p>’ is not supported (for information on implementing this, see the support forums) in /var/www/html/ojspujcali/lib/pkp/lib/vendor/ezyang/htmlpurifier/library/HTMLPurifier/HTMLDefinition.php on line 311, referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 21:07:47.211148 2018] [:error] [pid 26486] [client 127.0.0.1:35196] ojs2: 404 Not Found, referer: http://localhost/ojspujcali/index.php/pensamientopsicologico/issue/view/120

Thank you so much.
Really I need your help.

hi @asmecher, I try to change to PHP7.2 fro migration from 2.4 to 3.1 and I got the following warnings from Apache error.log file.

[Tue Oct 16 22:42:04.468616 2018] [php7:notice] [pid 13622] [client 127.0.0.1:49430] PHP Notice: A non well formed numeric value encountered in /var/www/html/ojspujcali/classes/install/Upgrade.inc.php on line 813, referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 22:42:04.470001 2018] [php7:notice] [pid 13622] [client 127.0.0.1:49430] PHP Notice: A non well formed numeric value encountered in /var/www/html/ojspujcali/classes/install/Upgrade.inc.php on line 813, referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 22:42:04.472931 2018] [php7:notice] [pid 13622] [client 127.0.0.1:49430] PHP Notice: A non well formed numeric value encountered in /var/www/html/ojspujcali/classes/install/Upgrade.inc.php on line 813, referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 22:42:04.474617 2018] [php7:notice] [pid 13622] [client 127.0.0.1:49430] PHP Notice: A non well formed numeric value encountered in /var/www/html/ojspujcali/classes/install/Upgrade.inc.php on line 813, referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 22:42:04.477459 2018] [php7:notice] [pid 13622] [client 127.0.0.1:49430] PHP Notice: A non well formed numeric value encountered in /var/www/html/ojspujcali/classes/install/Upgrade.inc.php on line 813, referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 22:42:07.028780 2018] [php7:warn] [pid 13622] [client 127.0.0.1:49430] PHP Warning: Declaration of SubmissionFileDAO::fromRow($row) should be compatible with PKPSubmissionFileDAO::fromRow($row, $fileImplementation) in /var/www/html/ojspujcali/classes/article/SubmissionFileDAO.inc.php on line 23, referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 22:42:46.956149 2018] [php7:notice] [pid 13622] [client 127.0.0.1:49430] WARNING: Unable to find a match for “1485-4335-1-SM.phtml” in “/var/www/submission_files/journals/1//articles/1485/”. Skipping this file., referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 22:42:47.227430 2018] [php7:notice] [pid 13622] [client 127.0.0.1:49430] WARNING: Unable to find a match for “1693-4954-1-SM.phtml” in “/var/www/submission_files/journals/1//articles/1693/”. Skipping this file., referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 22:42:47.232539 2018] [php7:notice] [pid 13622] [client 127.0.0.1:49430] WARNING: Unable to find a match for “1699-4979-1-SM.phtml” in “/var/www/submission_files/journals/1//articles/1699/”. Skipping this file., referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 22:42:47.234012 2018] [php7:notice] [pid 13622] [client 127.0.0.1:49430] WARNING: Unable to find a match for “1700-4981-1-SM.phtml” in “/var/www/submission_files/journals/1//articles/1700/”. Skipping this file., referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 22:42:47.278784 2018] [php7:notice] [pid 13622] [client 127.0.0.1:49430] WARNING: Unable to find a match for “1721-5060-1-SM.phtml” in “/var/www/submission_files/journals/1//articles/1721/”. Skipping this file., referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 22:45:55.402153 2018] [php7:notice] [pid 13622] [client 127.0.0.1:49430] PHP Notice: Only variables should be assigned by reference in /var/www/html/ojspujcali/lib/pkp/classes/filter/FilterHelper.inc.php on line 106, referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 22:45:55.431305 2018] [php7:notice] [pid 13622] [client 127.0.0.1:49430] PHP Notice: Only variables should be assigned by reference in /var/www/html/ojspujcali/lib/pkp/classes/filter/FilterHelper.inc.php on line 106, referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 22:45:55.432383 2018] [php7:notice] [pid 13622] [client 127.0.0.1:49430] PHP Notice: Only variables should be assigned by reference in /var/www/html/ojspujcali/lib/pkp/classes/filter/FilterHelper.inc.php on line 106, referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 22:45:55.433075 2018] [php7:notice] [pid 13622] [client 127.0.0.1:49430] PHP Notice: Only variables should be assigned by reference in /var/www/html/ojspujcali/lib/pkp/classes/filter/FilterHelper.inc.php on line 106, referer: http://localhost/ojspujcali/index.php/index/install/upgrade
[Tue Oct 16 22:45:56.042978 2018] [php7:warn] [pid 13622] [client 127.0.0.1:49430] PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/index/install/installUpgrade
[Tue Oct 16 22:45:56.434615 2018] [php7:warn] [pid 13626] [client 127.0.0.1:53422] PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/index/install/installUpgrade
[Tue Oct 16 22:45:56.460794 2018] [php7:warn] [pid 13626] [client 127.0.0.1:53422] PHP Warning: count(): Parameter must be an array or an object that implements Countable in /var/www/html/ojspujcali/cache/t_compile/e8ea13aa559bf8604ca823015b397a28d8666486^%%8B^8BC^8BC56207%%usernav.tpl.php on line 100, referer: http://localhost/ojspujcali/index.php/index/install/installUpgrade
[Tue Oct 16 22:47:57.531255 2018] [php7:warn] [pid 11230] [client 127.0.0.1:54248] PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0
[Tue Oct 16 22:47:57.698158 2018] [php7:warn] [pid 11230] [client 127.0.0.1:54248] PHP Warning: count(): Parameter must be an array or an object that implements Countable in /var/www/html/ojspujcali/cache/t_compile/65bfc3e024c2e9104f46e23b73376a9455e3df0e^%%41^413^413796DB%%indexSite.tpl.php on line 25
[Tue Oct 16 22:47:57.759956 2018] [php7:warn] [pid 11228] [client 127.0.0.1:54250] PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:48:00.842149 2018] [php7:warn] [pid 11256] [client 127.0.0.1:54256] PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:48:00.857356 2018] [php7:warn] [pid 11256] [client 127.0.0.1:54256] PHP Warning: Declaration of CustomBlockPlugin::getBlockContext() should be compatible with BlockPlugin::getBlockContext($contextId = NULL) in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:48:00.857436 2018] [php7:warn] [pid 11256] [client 127.0.0.1:54256] PHP Warning: Declaration of CustomBlockPlugin::getEnabled() should be compatible with BlockPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:48:00.857492 2018] [php7:notice] [pid 11256] [client 127.0.0.1:54256] PHP Notice: Only variables should be passed by reference in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockManagerPlugin.inc.php on line 65, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:48:00.893643 2018] [php7:notice] [pid 11256] [client 127.0.0.1:54256] PHP Notice: Only variables should be assigned by reference in /var/www/html/ojspujcali/pages/index/IndexHandler.inc.php on line 68, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:48:00.983240 2018] [php7:warn] [pid 11256] [client 127.0.0.1:54256] PHP Warning: Declaration of SubmissionFileDAO::fromRow($row) should be compatible with PKPSubmissionFileDAO::fromRow($row, $fileImplementation) in /var/www/html/ojspujcali/classes/article/SubmissionFileDAO.inc.php on line 23, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:48:01.122249 2018] [php7:warn] [pid 11256] [client 127.0.0.1:54256] PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/pensamientopsicologico
[Tue Oct 16 22:48:01.125539 2018] [php7:warn] [pid 11256] [client 127.0.0.1:54256] PHP Warning: Declaration of CustomBlockPlugin::getBlockContext() should be compatible with BlockPlugin::getBlockContext($contextId = NULL) in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/pensamientopsicologico
[Tue Oct 16 22:48:01.125553 2018] [php7:warn] [pid 11256] [client 127.0.0.1:54256] PHP Warning: Declaration of CustomBlockPlugin::getEnabled() should be compatible with BlockPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/pensamientopsicologico
[Tue Oct 16 22:48:01.125573 2018] [php7:notice] [pid 11256] [client 127.0.0.1:54256] PHP Notice: Only variables should be passed by reference in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockManagerPlugin.inc.php on line 65, referer: http://localhost/ojspujcali/index.php/pensamientopsicologico
[Tue Oct 16 22:51:24.011790 2018] [php7:warn] [pid 14702] [client 127.0.0.1:55652] PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:24.021102 2018] [php7:warn] [pid 14702] [client 127.0.0.1:55652] PHP Warning: Declaration of CustomBlockPlugin::getBlockContext() should be compatible with BlockPlugin::getBlockContext($contextId = NULL) in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:24.021125 2018] [php7:warn] [pid 14702] [client 127.0.0.1:55652] PHP Warning: Declaration of CustomBlockPlugin::getEnabled() should be compatible with BlockPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:24.021152 2018] [php7:notice] [pid 14702] [client 127.0.0.1:55652] PHP Notice: Only variables should be passed by reference in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockManagerPlugin.inc.php on line 65, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:24.036397 2018] [php7:notice] [pid 14702] [client 127.0.0.1:55652] PHP Notice: Only variables should be assigned by reference in /var/www/html/ojspujcali/pages/index/IndexHandler.inc.php on line 68, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:24.064272 2018] [php7:warn] [pid 14702] [client 127.0.0.1:55652] PHP Warning: Declaration of SubmissionFileDAO::fromRow($row) should be compatible with PKPSubmissionFileDAO::fromRow($row, $fileImplementation) in /var/www/html/ojspujcali/classes/article/SubmissionFileDAO.inc.php on line 23, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:24.185354 2018] [php7:warn] [pid 14702] [client 127.0.0.1:55652] PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/criteriojuridico
[Tue Oct 16 22:51:24.189144 2018] [php7:warn] [pid 14702] [client 127.0.0.1:55652] PHP Warning: Declaration of CustomBlockPlugin::getBlockContext() should be compatible with BlockPlugin::getBlockContext($contextId = NULL) in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/criteriojuridico
[Tue Oct 16 22:51:24.189170 2018] [php7:warn] [pid 14702] [client 127.0.0.1:55652] PHP Warning: Declaration of CustomBlockPlugin::getEnabled() should be compatible with BlockPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/criteriojuridico
[Tue Oct 16 22:51:24.189191 2018] [php7:notice] [pid 14702] [client 127.0.0.1:55652] PHP Notice: Only variables should be passed by reference in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockManagerPlugin.inc.php on line 65, referer: http://localhost/ojspujcali/index.php/criteriojuridico
[Tue Oct 16 22:51:30.975100 2018] [php7:warn] [pid 14702] [client 127.0.0.1:55652] PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:30.979742 2018] [php7:warn] [pid 14702] [client 127.0.0.1:55652] PHP Warning: Declaration of CustomBlockPlugin::getBlockContext() should be compatible with BlockPlugin::getBlockContext($contextId = NULL) in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:30.979774 2018] [php7:warn] [pid 14702] [client 127.0.0.1:55652] PHP Warning: Declaration of CustomBlockPlugin::getEnabled() should be compatible with BlockPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:30.979800 2018] [php7:notice] [pid 14702] [client 127.0.0.1:55652] PHP Notice: Only variables should be passed by reference in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockManagerPlugin.inc.php on line 65, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:30.990153 2018] [php7:notice] [pid 14702] [client 127.0.0.1:55652] PHP Notice: Only variables should be assigned by reference in /var/www/html/ojspujcali/pages/index/IndexHandler.inc.php on line 68, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:31.000793 2018] [php7:warn] [pid 14702] [client 127.0.0.1:55652] PHP Warning: Declaration of SubmissionFileDAO::fromRow($row) should be compatible with PKPSubmissionFileDAO::fromRow($row, $fileImplementation) in /var/www/html/ojspujcali/classes/article/SubmissionFileDAO.inc.php on line 23, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:36.017277 2018] [php7:warn] [pid 14702] [client 127.0.0.1:55652] PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/criteriojuridico
[Tue Oct 16 22:51:36.021658 2018] [php7:warn] [pid 14702] [client 127.0.0.1:55652] PHP Warning: Declaration of CustomBlockPlugin::getBlockContext() should be compatible with BlockPlugin::getBlockContext($contextId = NULL) in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/criteriojuridico
[Tue Oct 16 22:51:36.021693 2018] [php7:warn] [pid 14702] [client 127.0.0.1:55652] PHP Warning: Declaration of CustomBlockPlugin::getEnabled() should be compatible with BlockPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/criteriojuridico
[Tue Oct 16 22:51:36.021714 2018] [php7:notice] [pid 14702] [client 127.0.0.1:55652] PHP Notice: Only variables should be passed by reference in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockManagerPlugin.inc.php on line 65, referer: http://localhost/ojspujcali/index.php/criteriojuridico
[Tue Oct 16 22:51:36.024984 2018] [php7:warn] [pid 14702] [client 127.0.0.1:55652] PHP Warning: Declaration of ArticleHandler::initialize($request, $args) should be compatible with PKPHandler::initialize($request) in /var/www/html/ojspujcali/pages/article/ArticleHandler.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/criteriojuridico
[Tue Oct 16 22:51:36.027973 2018] [php7:notice] [pid 14702] [client 127.0.0.1:55652] ojs2: 404 Not Found, referer: http://localhost/ojspujcali/index.php/criteriojuridico
[Tue Oct 16 22:51:39.114581 2018] [php7:warn] [pid 11230] [client 127.0.0.1:55764] PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:39.118149 2018] [php7:warn] [pid 11230] [client 127.0.0.1:55764] PHP Warning: Declaration of CustomBlockPlugin::getBlockContext() should be compatible with BlockPlugin::getBlockContext($contextId = NULL) in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:39.118223 2018] [php7:warn] [pid 11230] [client 127.0.0.1:55764] PHP Warning: Declaration of CustomBlockPlugin::getEnabled() should be compatible with BlockPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:39.118263 2018] [php7:notice] [pid 11230] [client 127.0.0.1:55764] PHP Notice: Only variables should be passed by reference in /var/www/html/ojspujcali/plugins/generic/customBlockManager/CustomBlockManagerPlugin.inc.php on line 65, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:39.125756 2018] [php7:notice] [pid 11230] [client 127.0.0.1:55764] PHP Notice: Only variables should be assigned by reference in /var/www/html/ojspujcali/pages/index/IndexHandler.inc.php on line 68, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:39.136997 2018] [php7:warn] [pid 11230] [client 127.0.0.1:55764] PHP Warning: Declaration of SubmissionFileDAO::fromRow($row) should be compatible with PKPSubmissionFileDAO::fromRow($row, $fileImplementation) in /var/www/html/ojspujcali/classes/article/SubmissionFileDAO.inc.php on line 23, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:45.034395 2018] [php7:warn] [pid 11228] [client 127.0.0.1:55804] PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:45.050198 2018] [php7:notice] [pid 11228] [client 127.0.0.1:55804] PHP Notice: Only variables should be assigned by reference in /var/www/html/ojspujcali/pages/index/IndexHandler.inc.php on line 68, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:45.066120 2018] [php7:warn] [pid 11228] [client 127.0.0.1:55804] PHP Warning: Declaration of SubmissionFileDAO::fromRow($row) should be compatible with PKPSubmissionFileDAO::fromRow($row, $fileImplementation) in /var/www/html/ojspujcali/classes/article/SubmissionFileDAO.inc.php on line 23, referer: http://localhost/ojspujcali/
[Tue Oct 16 22:51:45.119036 2018] [php7:warn] [pid 11228] [client 127.0.0.1:55804] PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/revistamaestro
[Tue Oct 16 22:51:48.216956 2018] [php7:warn] [pid 13900] [client 127.0.0.1:55816] PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/revistamaestro
[Tue Oct 16 22:51:48.560259 2018] [php7:warn] [pid 13900] [client 127.0.0.1:55816] PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/revistamaestro/issue/archive
[Tue Oct 16 22:51:50.875201 2018] [php7:warn] [pid 13900] [client 127.0.0.1:55816] PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/revistamaestro/issue/archive
[Tue Oct 16 22:51:50.904065 2018] [php7:warn] [pid 13900] [client 127.0.0.1:55816] PHP Warning: Declaration of SubmissionFileDAO::fromRow($row) should be compatible with PKPSubmissionFileDAO::fromRow($row, $fileImplementation) in /var/www/html/ojspujcali/classes/article/SubmissionFileDAO.inc.php on line 23, referer: http://localhost/ojspujcali/index.php/revistamaestro/issue/archive
[Tue Oct 16 22:51:50.951773 2018] [php7:warn] [pid 13900] [client 127.0.0.1:55816] PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/revistamaestro/issue/view/102
[Tue Oct 16 22:51:52.991638 2018] [php7:warn] [pid 13900] [client 127.0.0.1:55816] PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/revistamaestro/issue/view/102
[Tue Oct 16 22:51:52.997323 2018] [php7:warn] [pid 13900] [client 127.0.0.1:55816] PHP Warning: Declaration of ArticleHandler::initialize($request, $args) should be compatible with PKPHandler::initialize($request) in /var/www/html/ojspujcali/pages/article/ArticleHandler.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/revistamaestro/issue/view/102
[Tue Oct 16 22:51:52.998865 2018] [php7:notice] [pid 13900] [client 127.0.0.1:55816] ojs2: 404 Not Found, referer: http://localhost/ojspujcali/index.php/revistamaestro/issue/view/102
[Tue Oct 16 22:51:56.149501 2018] [php7:warn] [pid 11257] [client 127.0.0.1:55900] PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/revistamaestro/issue/archive
[Tue Oct 16 22:51:56.170843 2018] [php7:warn] [pid 11257] [client 127.0.0.1:55900] PHP Warning: Declaration of SubmissionFileDAO::fromRow($row) should be compatible with PKPSubmissionFileDAO::fromRow($row, $fileImplementation) in /var/www/html/ojspujcali/classes/article/SubmissionFileDAO.inc.php on line 23, referer: http://localhost/ojspujcali/index.php/revistamaestro/issue/archive
[Tue Oct 16 22:51:58.566813 2018] [php7:warn] [pid 11257] [client 127.0.0.1:55900] PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/html/ojspujcali/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0, referer: http://localhost/ojspujcali/index.php/revistamaestro

Hi @Juan_Pablo_Giron_Rui,

It’s OK to get lots of warnings from the upgrade process – it looks like you have PHP’s strict mode enabled, which will result in lots of complaints that won’t affect the outcome. What was the final result? Did you get a success or failure message at the end?

Regards,
Alec Smecher
Public Knowledge Project Team

Hi @asmecher, the problem is that when I try to open the file, the path is incorrect and appear the message 404 file not found. I try to find the script where the submission_files is changed in OJS3 upgrade process, but I could not luck.

I try to install inside line command using php tools\upgrade.php upgrade in su mode. I thought that problem was in OS (Initially I installed on windows) but it is not.

cheer,
Juan Pablo

Excuse me, I dont replied your questions.

What was the final result? That was all response from Apache error.log file.

Did you get a success or failure message at the end? I get the message that upgrade was succesful, but I did not get an error message.

thanks you.

PD. My project is in /var/www/html/ojs

the ojs folder has 777 permissions in all sub-directories and files.

My submission_files is in /var/www/. Also, this has 777 permissions.

I am using php5.6 as prinicipal PHP version on Ubuntu 18 with mariaDB 10 version.

Hi @Juan_Pablo_Giron_Rui,

Note that 777 permissions are never safe to use in production; they can be helpful for debugging but you should change them to something more secure ASAP.

Also note that putting your files_dir inside your web root is unsafe (unless you’ve protected it from direct access e.g. using a .htaccess file) and if you don’t fix this you will get hacked. There are more details on this in the “Recommended Configuration” section of docs/README.

Does your files_dir still contain filenames like 1-85-1-PB.pdf (rather than longer names e.g. 14-1-26-1-10-20180312.pdf)? If so, then the upgrade process still wasn’t able to rename your files during upgrade. You can resolve this by restoring your files and database from backup, double-checking that your files_dir and file permissions are correct before running the upgrade, and trying it again.

Regards,
Alec Smecher
Public Knowledge Project Team

Hi @asmecher

my filenames has a reasonable length name. For example:

image

image

This paper can be visualized in: http://revistas.javerianacali.edu.co/index.php/pensamientopsicologico/article/view/1758/2488

The same paper in OJS3 appears as File not Found.

When you say “double-checking that you files_fir and file permissions are correct …” is give the submission_folder chmod -R 0755 permission?

On the other hand, the recommend configuration section in docs/README file says…

Install OJS so that the files directory is NOT a subdirectory of
the OJS installation and cannot be accessed directly via the web
server. Restrict file permissions as much as possible. Automated
backups of this directory should be roughly synchronized with
database backups.

Where exactly should be submission_files? In /var/?

thanks you @asmecher for your help.

Hi @Juan_Pablo_Giron_Rui,

Yes, a subdirectory of /var would be a good place to keep your files directory.

The filename above (1758-6135-1-PB.pdf) is still an OJS 2.x style filename. This means that the upgrade process couldn’t rename it, because the files_dir wasn’t correctly set in config.inc.php, or file permissions wouldn’t allow it to be renamed, or something similar.

Details on file permissions will depend on your server; see How should file permissions be set? for details.

Regards,
Alec Smecher
Public Knowledge Project Team

Hello @asmecher,

I did some changes at database migration process. Now I have my data in MariaDB. I’ve tried (again) to migrate from ojs 2.3 to ojs 3.1 using ojs 2.4 as bridge. When I run my upgrade using php tool/upgrade.php upgrade I am obtaining the next error:

(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 = ‘es_ES’)
LEFT JOIN section_settings stl ON (se.section_id = stl.section_id AND stl.setting_name = ‘title’ AND stl.locale = ‘es_ES’)
LEFT JOIN section_settings sapl ON (se.section_id = sapl.section_id AND sapl.setting_name = ‘abbrev’ AND sapl.locale = ‘es_ES’)
LEFT JOIN section_settings sal ON (se.section_id = sal.section_id AND sal.setting_name = ‘abbrev’ AND sal.locale = ‘es_ES’)
WHERE s.submission_id = 397

-----



-----

(mysql): SELECT * FROM submission_settings WHERE submission_id = ‘397’

-----



PHP Warning: assert(): Assertion failed in /var/www/html/ojs3/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php on line 112
PHP Warning: mkdir(): Permission denied in /var/www/html/ojs3/lib/pkp/classes/file/FileManager.inc.php on line 289
PHP Warning: copy(/var/submission_files3/journals/1//articles/397/submission/review/397-38–1-4-20121003.doc): failed to open stream: Permission denied in /var/www/html/ojs3/lib/pkp/classes/file/FileManager.inc.php on line 159
-----

(mysql): DELETE FROM submission_files
WHERE file_id = 6216 AND revision = 1

-----



-----

(mysql): SELECT * FROM submission_files WHERE file_id = 6216

-----



-----

(mysql): DELETE FROM submission_file_settings WHERE file_id = 6216

-----



-----

(mysql): DELETE FROM item_views WHERE assoc_type = 515 AND assoc_id = ‘6216-1’

-----



-----

(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 = ‘es_ES’)
LEFT JOIN section_settings stl ON (se.section_id = stl.section_id AND stl.setting_name = ‘title’ AND stl.locale = ‘es_ES’)
LEFT JOIN section_settings sapl ON (se.section_id = sapl.section_id AND sapl.setting_name = ‘abbrev’ AND sapl.locale = ‘es_ES’)
LEFT JOIN section_settings sal ON (se.section_id = sal.section_id AND sal.setting_name = ‘abbrev’ AND sal.locale = ‘es_ES’)
WHERE s.submission_id = 397

-----



-----

(mysql): SELECT * FROM submission_settings WHERE submission_id = ‘397’

-----



PHP Fatal error: Call to a member function getFileId() on null in /var/www/html/ojs3/lib/pkp/classes/submission/PKPSubmissionFileDAO.inc.php on line 1065

I don’t know what registries I have to verify before I run the upgrade script. Can you help me please?

thanks in advance.

Hi @Juan_Pablo_Giron_Rui,

I see you’ve also followed up on this at When trying to update my Ojs from version 2.4.2.3 to Ojs 3.x then this log appears a blank screen with no functionality. Does anyone know why this? - #10 by Juan_Pablo_Giron_Rui – I’d suggest continuing along the lines discussed there. (If you do post the same issue in two places, please make sure you link them together to help keep the forum organized – but better to post in just one place.)

Regards,
Alec Smecher
Public Knowledge Project Team

how to upload from localhost to server? After upload site warning " There are no readable files in this directory tree. Are safe mode or open_basedir active?" how to solved url change?

Hi @it.feb,

I see this is also posted here: Missing file upgared OJS 2.4 to 3.1 - #4 by it.feb

Please try not to post the same content in multiple places; it clutters the forum.

Thanks,
Alec Smecher
Public Knowledge Project Team

Hi Juan,
I already see you link and it seems the ojs is working fine. My upgrade from 2.4.8.1 also get same problem, one of my files is missing. Is there any clue how you can solve this issue?

I already try many upgrade but still missing. Please, really need this help.

Regards,
Viper.