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All issues "lost" after upgrade 2.3.1.0 to 2.4.2.0

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What to do if you have a technical problem with OJS:

1. Search the forum. You can do this from the Advanced Search Page or from our Google Custom Search, which will search the entire PKP site. If you are encountering an error, we especially recommend searching the forum for said error.

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Re: All issues "lost" after upgrade 2.3.1.0 to 2.4.2.0

Postby asmecher » Mon Jun 24, 2013 9:58 am

Hi Carlos,

The error message about mysql_pdo.so is a server configuration problem unrelated to OJS -- probably your php.ini references this file and it doesn't exist on your server. Either way, it's unlikely to prevent OJS from working, but should probably be cleaned up.

As for the failed assertions in DBDataXMLParser.inc.php, this sounds to me like a case where the upgrade is attempting to rename a column, but the column doesn't actually exist. Check your pre-upgrade database to make sure that the following columns exist:
  • review_forms.journal_id
  • article_files.type
  • article_email_log.article_id
  • review_assignments.article_id
  • review_rounds.article_id
  • comments.article_id
  • article_notes.article_id
  • article_notes.note
  • article_authors.article_id
Regards,
Alec Smecher
Public Knowledge Project Team
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Re: All issues "lost" after upgrade 2.3.1.0 to 2.4.2.0

Postby CFreire » Mon Jun 24, 2013 10:47 am

Hi Alec:

All columns exist in pre-upgrade database.
Now, after attempting to upgrade, none. Nor tables "article_email_log", "article_notes" and "article_authors".

I'm checking with the server about the file mysql_pdo.so.

And now? I'm getting really worried...

Regards,

Carlos
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Re: All issues "lost" after upgrade 2.3.1.0 to 2.4.2.0

Postby asmecher » Mon Jun 24, 2013 11:01 am

Hi Carlos,

Can you turn on the "debug" option before running the upgrade? That'll allow me to figure out where in the upgrade process it's failing.

Regards,
Alec Smecher
Public Knowledge Project Team
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Re: All issues "lost" after upgrade 2.3.1.0 to 2.4.2.0

Postby CFreire » Mon Jun 24, 2013 11:20 am

Ok... I will:
- Restore the backup;
- Reinstall the upgrade -> with debug option "on" and the "migration codes" (dbscripts/xml/upgrade.xml) activated this time.

In time: in "user_settings" table, was a duplicate entries in setting_name "biography". It's a problem?

Carlos
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Posts: 68
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Re: All issues "lost" after upgrade 2.3.1.0 to 2.4.2.0

Postby CFreire » Mon Jun 24, 2013 7:57 pm

Hi, Alec

I d'ont believe...

Process time: 2 pm to 11:30 pm;
Result:
Fatal error: Allowed memory size of 268435456 bytes exhausted (tried to allocate 40 bytes) in /periodicos.proped.pro.br/www/lib/pkp/lib/adodb/adodb-lib.inc.php on line 950

Last table edited: "notifications" (more or less 5h entering data);
Last command:
(mysql): INSERT INTO notifications (user_id, level, date_created, date_read, context_id, type, assoc_type, assoc_id) VALUES ....

Table notifications_old: 146.526 rows;
Table notifications: 143.339 rows;
*#*!$#uck! :x

There has to be an easier way (or least time consuming)? Some command line that I can ask the support of my server? Those who tried ssh-client (patch), never worked.

Regards,
Carlos
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Re: All issues "lost" after upgrade 2.3.1.0 to 2.4.2.0

Postby asmecher » Tue Jun 25, 2013 8:01 am

Hi Carlos,

That's a shame -- it looks like it was just about to complete, judging by the row counts. There are several solutions you could try:Regards,
Alec Smecher
Public Knowledge Project
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Posts: 8470
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Re: All issues "lost" after upgrade 2.3.1.0 to 2.4.2.0

Postby CFreire » Tue Jun 25, 2013 8:53 am

Thanks for the solidarity, Alec...

If I understood:
- restore database from backup;
- truncate notifications table;
- increase php memory limit;
- apply the diff patch;
- cross my fingers;
- reinstall upgrade;

8) No need to reply if I'm right... I'll try this only tonight (Brazilian time).

Thanks again, regards,

Carlos
CFreire
 
Posts: 68
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Re: All issues "lost" after upgrade 2.3.1.0 to 2.4.2.0

Postby asmecher » Tue Jun 25, 2013 9:05 am

Hi Carlos,

That's all three solutions at once, when probably any one of them would work -- but yes, that should get you past the notifications upgrade that you're having trouble with.

Cheers,
Alec Smecher
Public Knowledge Project Team
asmecher
 
Posts: 8470
Joined: Wed Aug 10, 2005 12:56 pm

Re: All issues "lost" after upgrade 2.3.1.0 to 2.4.2.0

Postby CFreire » Tue Jun 25, 2013 10:08 am

Thanks Alec, but...

Could you - please - explain better your last sentence ("but yes, that should...")?
My sioux-google-english is very limited... :oops:

Cheers,
Carlos
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Posts: 68
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Re: All issues "lost" after upgrade 2.3.1.0 to 2.4.2.0

Postby asmecher » Tue Jun 25, 2013 10:17 am

Hi Carlos,

No problem. I meant that any one of the three solutions I suggested should be enough. If you do all three, you should be fine, but it's not necessary to do them all.

Regards,
Alec Smecher
Public Knowledge Project Team
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Posts: 8470
Joined: Wed Aug 10, 2005 12:56 pm

Re: All issues "lost" after upgrade 2.3.1.0 to 2.4.2.0

Postby CFreire » Thu Jun 27, 2013 12:19 pm

Hi Alec:

Wary, I decided to do the two options (I can't increase the memory php).
First, the patch:

1) Deleted the references - in the patch - to the directories "a" and "b" (lines 1-4);
2) Applied the patch;
Return:
vhost13:~/www/lib/pkp$ patch classes/plugins/HookRegistry.inc.php patch_OJS.diff
patching file classes/plugins/HookRegistry.inc.php
Hunk #1 FAILED at 68.
Hunk #2 FAILED at 97.
2 out of 2 hunks FAILED -- saving rejects to file classes/plugins/HookRegistry.inc.php.rej
can't find file to patch at input line 76
Perhaps you should have used the -p or --strip option?
The text leading up to this was:
--------------------------
|diff --git a/tests/classes/core/PKPRequestTest.php b/tests/classes/core/PKPRequestTest.php
|index c38159f..a0a2eee 100644
|--- a/tests/classes/core/PKPRequestTest.php
|+++ b/tests/classes/core/PKPRequestTest.php


If I used -p option:
File to patch: patch -p classes/plugins/HookRegistry.inc.php patch_OJS.diff
patch: No such file or directory
Skip this patch? [y] y
Skipping patch.
1 out of 1 hunk ignored
can't find file to patch at input line 88
Perhaps you should have used the -p or --strip option?
The text leading up to this was:
--------------------------
|diff --git a/tests/classes/core/PKPRouterTestCase.inc.php b/tests/classes/core/PKPRouterTestCase.inc.php
|index a8d678e..4601c7c 100644
|--- a/tests/classes/core/PKPRouterTestCase.inc.php
|+++ b/tests/classes/core/PKPRouterTestCase.inc.php


If I delete the lines from the 72 (diff - git a / tests ...), return:
Hunk # 1 FAILED at 32.
Hunk # 2 FAILED at 112.
patch unexpectedly ends in middle of line
patch: **** unexpected end of file in patch


I checked the original file (HookRegistry.inc.php) and did not see any change, even in the early part of that, in theory, should have been applied ... or not?

In time, I'm considering:
- Make a backup of the current table "notifications" (just interrupted missing a few lines);
- Restore it after migration (performed with the first table "notifications" truncated, according to your instructions).
It would be a good idea?

Regards, Carlos
Attachments
HookRegistry.inc.php.rej.pdf
(16.04 KiB) Downloaded 13 times
CFreire
 
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Re: All issues "lost" after upgrade 2.3.1.0 to 2.4.2.0

Postby asmecher » Thu Jun 27, 2013 2:06 pm

Hi Carlos,

That patch should be applied from within the lib/pkp subdirectory with the -p1 option specified to the patch tool. (If you've removed the a/ and b/ parts of the patch file, then -p0 should work instead.)

You won't be able to restore the notifications table after upgrading because its structure has changed -- the part of the upgrade that failed was converting the data from one format to the other.

Regards,
Alec Smecher
Public Knowledge Project Team
asmecher
 
Posts: 8470
Joined: Wed Aug 10, 2005 12:56 pm

Re: All issues "lost" after upgrade 2.3.1.0 to 2.4.2.0

Postby CFreire » Thu Jun 27, 2013 5:05 pm

Yes, I always applied the patch from lib/pkp.
Now, I reused original patch (with a/ and b/), with the command:

patch -p1 classes/plugins/HookRegistry.inc.php patch_OJS.diff

Result:
patching file classes/plugins/HookRegistry.inc.php
Hunk #1 FAILED at 68.
Hunk #2 FAILED at 97.
2 out of 2 hunks FAILED -- saving rejects to file classes/plugins/HookRegistry.inc.php.rej
can't find file to patch at input line 76
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|diff --git a/tests/classes/core/PKPRequestTest.php b/tests/classes/core/PKPRequestTest.php
|index c38159f..a0a2eee 100644
|--- a/tests/classes/core/PKPRequestTest.php
|+++ b/tests/classes/core/PKPRequestTest.php

If the patch does not work, left me only "truncate table" :( ... [and cross fingers after special-saravá's-macumba-on-computer-against-Murphy].

Regards, Carlos
Attachments
HookRegistry.inc.php.rej.pdf
(16.04 KiB) Downloaded 13 times
CFreire
 
Posts: 68
Joined: Sun Aug 12, 2007 7:39 pm

Re: All issues "lost" after upgrade 2.3.1.0 to 2.4.2.0

Postby asmecher » Fri Jun 28, 2013 8:51 am

Hi Carlos,

Alternately, you ought to be able to download the new version of HookRegistry.inc.php from https://github.com/pkp/pkp-lib/blob/ojs-stable-2_4/classes/plugins/HookRegistry.inc.php; replace the existing copy in lib/pkp/classes/plugins with the new copy.

Regards,
Alec Smecher
Public Knowledge Project Team
asmecher
 
Posts: 8470
Joined: Wed Aug 10, 2005 12:56 pm

Re: All issues "lost" after upgrade 2.3.1.0 to 2.4.2.0

Postby CFreire » Sat Jun 29, 2013 10:18 am

Hi Alec, it worked!

I used both options, truncate notifications table and new version of HookRegistry.inc.php(*).
2 attempts (one Murphy blackout in the middle of the first) and "only" 5 hours later, via web ... and done.

Final notes.
I think the difficulties and the time spent in the process are:
1) a direct consequence of the jump of 16 versions [conclusion: never expect agreement from all publishers to upgrade];
2) my mistake to use the recommended patch from version 2.3.1, when the correct thing from version 2.3.3-2.
3) at least I learned how to access the php via ssh comand line on my server - and this will be my next upgrade option. If it will work or not ... 8)

(*) But what worked, I bet, was the crossing of fingers and Saravá! :D

Last but..., thanks a lot - extensive to PKP Team - for the support and patience.

Cheers, Carlos
CFreire
 
Posts: 68
Joined: Sun Aug 12, 2007 7:39 pm

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