Sunday, April 23, 2006

Darwin hacked

One of my lab's web servers was hacked last week. This machine hosts a lot of projects, such as the Glasgow Name Server, the Taxonomic Search Engine, iSpecies, LouseBase, and TreeView X. Sadly, it was not completely backed up, although most of the key stuff is replicated elsewhere (including source code in CVS on another machine, or in SourceForge, copies of databases on other machines, etc.). Even if it was completely backed up, there is the hassle of rebuilding a machine. Still, since it wasn't backed up, here are some of the things I had to go through.


The kernel (Red Hat 8) had been tampered with, so the machine would no longer boot. I'm was now faced with the task of getting stuff off the machine in case reinstalling the operating system lost data. Luckily the machine (a Dell Precision 620) booted from a Knoppix CD, which gave me a GUI. So now I can browse my crippled machine, but...

... it couldn't talk to the Net because the Knoppix live CD uses DHCP to get an IP address, and my university doesn't support DHCP (argh!). However, I have an Apple Airport base station with a spare Ethernet port, and connecting the Dell to that port provided a DHCP address (yay).

Booting from a live CD has one major limitation -- I can't alter anything on the disks in the Dell. Hence, doing things like changing file permissions, or making tarballs to be able to FTP directories is out of the question. I don't have a USB key or an external USB hard drive big enough to take the gigabytes of stuff on the Dell.

What worked, after a lot of fussing was Samba. Using the smb:// protocol in Konqueror (I trick I learned from Mac OS X), I managed to connect to a Fedora Core 4 box in my lab. I could then drag and drop key files onto the FC4 machine (such as httpd.conf, hosts.allow, various CGI scripts, etc.) that were specific to the hacked machine. I also made backups of the home folders, just in case.

This left MySQL databases. Moving these proved to be a major pain, because they are not accessible by the Knoppix user. The solution turned out to be to mount the FC4 box using Samba:


  1. su

  2. mkdir /mnt/linnaeus

  3. mount -t smbfs -o username=xxxx //linnaeus.zoology.gla.ac.uk/xxxx /mnt/linnaeus



Now we can copy all the MySQL databases on the FC4 machine.

Ah, but how to get the actual data...? Well, on my Mac OS 10.3 iBook, I have MySQL 4.0.21, which works with the MySQL files from Red Hat 8 (3.23 I think). I use CocoaSQL to create the database, then move all the .MYI and .MYD files into the appropriate folder in /Library/MySQL/data/, then set permissions to ensure that mysql can read the files (make user mysql the owner chown mysql *, and set permissions to 660).

Yes, the obvious lesson is to have everything backed up, but on a developmental machine with gigabytes of images and other data, much of it moved around frequently, and a central backup system whose client software wouldn't build on my machine, I'd sort of let this slip (doh!).

1 comment:

Sadie said...

In a similar set of chaotic circumstances, I failed to back up my bookmarks when last exploring phylogenetics on the web and can no longer track down the supertree via your site. Grrr. Good luck resurrecting all the connections and restoring this fantastic resource.