By somatics on

We attempted to upgrade our Drupal installation from 6.8 to 6.19 today and all we are getting now are a lot of different fatal errors. I can't find any posts on this that tell me anything definitive except that it may be corruption.

We've worked on this non stop all day -- repairing the database to the best of our ability, removing modules, etc. -- and are at a dead end. We are in real trouble here and need someone who has some experience working with corrupted databases, and we need it done right away. Is there anyone available to work on this right away? Please help!!

Here's a brief synopsis of more details:

We put in version 6.19, ran the Upgrade script, got some error messages I can show you, but the system worked fine. Then I put in all the new versions of modules needed, went to update.php in my browser, got a notice I was missing the fbconnect folder, copied it from a backup and refreshed the update page before clicking the update button -- and that's where everything went wrong. I started getting WSOD. When I made it show error messages, I've gotten lots of different ones all day; some of them include:

Fatal error: Call to undefined function _system_theme_data() in /path/to/drupal6/includes/theme.inc on line 481

Fatal error: Call to undefined function filter_xss_admin() in /path/to/drupal6/sites/all/modules/ctools/page_manager/plugins/tasks/page.inc on line 205

Fatal error: Call to undefined function user_access() in /path/to/drupal6/includes/menu.inc on line 449

⋅ Categories: Drupal 6.x

Comments

onejam’s picture

onejam commented

You are probably missing some contrib module files that didn't get properly copied over.

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We build engaging websites and intuitive designs that will benefit your business.
Duvien

snufkin’s picture

snufkin commented

actually this looks like he did not copy core correctly as he is missing functions like user_access.

littlegreencube’s picture

littlegreencube commented

somatics: we're seeing the exact same thing on one of our sites. upgraded a module this morning and everything is down. the error message changes but always says something like

Fatal error: Call to undefined function _system_theme_data() in /includes/theme.inc on line 481

have you made any progress on your site?

onejam’s picture

onejam commented

I've had cases where for some odd reason activated contrib modules got disabled during the upgrade causing the core not to be able to find certain modules dependencies. I suggest, you disable all modules and then do your upgrade and turn each of them back on after upgrade.

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We build engaging websites and intuitive designs that will benefit your business.
Duvien

criznach’s picture

criznach commented

Did you remove the old modules before uploading the updates? I've seen cases where a file path changed, and the remaining files caused duplicate or missing functions.

http://www.trailheadinteractive.com

shane birley’s picture

shane birley commented

...dump the cache tables? If you don't empty the cache tables prior to an upgrade (not every time, but it does help) you can get references to old non-updated tables in the database that will blank the site.

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Shane Birley
Left Right Minds
https://www.leftrightminds.com

somatics’s picture

somatics commented

I did truncate or empty the cache tables after I encountered this problem, and it didn't seem to help. Thanks though!

My other post on this in this topic will tell you where this situation is at now.

somatics’s picture

somatics commented

Thank you everyone for this great advice. It seems like many of these might be part of the solution to what I was encountering. I've made some progress on it by going in a different direction -- and I think it's almost fixed, but I've hit a new roadblock and I'm stuck again right near probably the finish line. I'm hoping one of you has a solution to this issue:

The database has now been restored to it's original Drupal 6.8 state from before the upgrade attempt.

(I'm still going to want to upgrade from 6.8 to 6.19 and to all the current modules version, but I think it's better to start that process fresh and perhaps still to hire someone to do the upgrade to make sure there is no problem causing corruption during upgrade; so for now, I need the original version back up and running fully, asap).

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But now the apparent problem is the database has become READ ONLY!
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Here are the details:

Very late last night, I realized there might in fact be a successful backup of the mySQL database stored in Time Machine on my OS X 10.6 Xserve (when I first posted this issue, it appeared the Time Machine backup was gone). This morning I...

1) Navigated within the Time Machine backup via command line as sudo.

2) Found the most recent backup (of the Drupal 6.8 version of the database -- from early yesterday before I started trying to update to 6.19)

3) Copied it over to the /var/mySQL directory in place of the potentially corrupted version (renaming the corrupted one first, of course). I used the ditto command instead of the cp command, as they are supposedly the same now but ditto defaults to an exact copy whereas cp requires a few qualifiers.

4) I also replaced the Drupal folder with the 6.8 version I had been using that matched the backup database.

Our website launched seemingly perfectly with no problems. Then I tried to login... Drupal would take the password, but then send me back to the login screen with no errors. A few hours of experiments and research later, and, as I said, it appears that the problem is the database is now read only.

Drupal can't write to the sessions database (or anything else for that matter), so it doesn't complete the login.

Here's the error message:


Can't create/write to file '/private/var/mysql/dp_somatics/sessions.MYI' (Errcode: 13)

[Insert whatever table name you want -- it does it for all of them.]

I tried other databases on this mySQL server, and they all seem to read and write just fine.

* I tried repairing individual tables (Navicat -- the GUI mySQL admin program I'm using -- claims the repair is done). I tried truncating and/or dropping individual tables (which it can't do, since it's read only).

* I read one site that said to try to make a backup of it, as that should unlock it, so I tried that with no success. Rebooting didn't help.

* It also doesn't seem to have anything to do with the /var/tmp directory (which some websites said it might), as the server can seemingly write to that -- this is a problem with the database itself not being writable, not the tmp directory.

* Some sites say it has to do with permissions, but the permissions seem fine within mySQL, and the file level permissions say the owner is mySQL with read/write access and everybody else has no access -- just like all the other mySQL databases and files.

* Some sites say it means a corrupt database, but this kind of corruption can just be repaired and the database will be back to normal with no data issues. I don't know how to do this, and oddly enough searching on this error message pulls up a lot of "almosts", but no solid lead as to what to do.

Soooooooo, I'm stuck, and I"ve got to get this thing full functional asap, as we are making a major announcement in a few hours that requires the writeable website.

Do any of you have any idea what to do? I have tried for hours and cannot find a website that will tell me what i need to know to fix this.

sreyas’s picture

sreyas commented

1. As you have a backup of the database, create a new database and import it using mysql import or navicat.
2. Update the drupal settings.php db_url with this new database information.
3. If you are doing it correct then there is no reason for getting it locked, if it still does then better find out a good db admin!!

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Ciril Sreedhar
Sreyas IT Solutions
Server Administration | Web Designing | Web Programming

somatics’s picture

somatics commented

Yes, I thought of doing this a few hours after I made my post -- I feel like an idiot that it didn't occur to me at the time. I think it just took a little while for my brain to go through all the possible avenues within mySQL -- as I am *not* a seasoned mySQL admin.

So, I did the backup: What I actually did was use the Data Transfer feature on Navicat (it's a GUI admin app for mySQL). I created a fresh database, and transferred the entire structure and data contents of the read only db to the new db.

It took almost a day, as the Cache & Watchdog tables hung up for hours each. I stopped the transfer each time, and found the all the data for each table had been transferred, but those two tables each seemed to be screwed up in someway so they behaved as if they each had another few gigabytes of records in them. I then performed another transfer of the tables not yet transferred over. (Navicat is such a great program. If anyone isn't familiar with it and needs to deal with their database, I strongly recommend it.)

Once it completed, the new database is read and write, the site works as normal, and everything seems to be happy.

Now, I just have the regular bugs in Drupal throwing me for a loop and delaying launch of the site! So, back to the trenches!!

Thanks again for all your help!