Say I am working outside the office firewall, on a machine called home, and I need to get into a MySQL server inside it. (Doesn’t have to be MySQL, but just for argument’s sake.)

There’s a machine called gateway I can ssh to and tunnel through, but for security reasons, the database server mysql doesn’t accept connections from gateway directly. But my desktop machine at the office (err… desktop) can connect to mysql.

One way round it is to ssh from home to gateway and forward a port on gateway to the ssh server on desktop:

home $ ssh -L 2222:desktop.example.org:22 -tAY gateway.example.org

And then in another terminal, ssh from home to desktop via this tunnel, forwarding another port on home to the incoming connections port on mysql (3306 in MySQL’s case usually):

home $ ssh -p 2222 -L 23306:mysql.example.org:3306 127.0.0.1

This time, you’re connecting to home port 2222, but because of the first command, this forwards you straight to desktop port 22.

Now both tunnels are in place, you can just connect to port 23306 on home and arrive by magic at mysql. In another terminal (or from your MySQL GUI):

home $ mysql -uUSER -pPASS -h127.0.0.1 -P23306

This example shows a tunnel-within-a-tunnel. There should be a way to make this work using end-to-end tunnelling instead, I tried but didn’t get anywhere. But that might be due to ssh server restrictions on our equivalent of gateway.

If none of this means anything, there’s an intro to ssh port forwarding here.

I have two network interfaces in my Ubuntu guest (on OS X 10.4 host), one NAT, one host-only.

Sometimes one of them doesn’t get an IP address — in ifconfig it has an inet6 address but not an inet address.

Today I tried

sudo dhclient eth1

and it worked — all it needed to do was re-query VirtualBox’s built-in DHCP server.

I would have thought this would do that automatically:

sudo /etc/init.d/networking restart

However that didn’t help… But dhclient did.

Another recurring problem is that when I move between different networks, DNS resolution gets screwed up. There’s a description of this with a suggested work around (using VBox’s DNS Proxy) here:

http://forums.virtualbox.org/viewtopic.php?f=1&t=28332

However, while this seemed to help with two of the networks I use frequently, it didn’t with a third, even after rebooting.

So, as suggested on one or two threads, I’ve removed the DNSProxy setting, and set the Ubuntu guest to use Google’s public DNS servers instead of those provided by the DHCP server for the NATted virtual NIC. (Blah blah blah.) Follow example here (more or less):

http://grumpymole.posterous.com/how-to-use-google-public-dns-or-opendns-in-ub

Seems to be working so far… But only tested on one of the offending networks, and without rebooting yet. Updates to come later.

… Nope, after upgrading to Snow Leopard and the latest VirtualBox (it’s now from Oracle — scary), random problems persist.

Sometimes I’ll lose guest-host connectivity in the middle of a session, without any sleep or other interruptions, but will still be able to see the internet from the NAT adaptor.

One possible solution here involving using OS X itself as the NAT router:

http://akutz.wordpress.com/2009/08/20/building-a-better-os-x-firewall-or-how-i-solved-the-nat-problem-for-virtualbox/

… but it’ll take work.

Or maybe a simpler version of the same approach: have a single host-only adaptor, use OS X’s internet sharing to share the AirPort card, and manually tell the vbox to use 192.168.56.1 as the default gateway:

http://forum.virtualbox.org/viewtopic.php?f=1&t=26544

If all else fails, try using a different ethernet hardware emulator.

So I’ve replaced my iTunes Dock icon with a little AppleScript that checks whether said disk is mounted first:

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tell application "Finder"
	if exists (disk "LaCie") then
		tell application "iTunes" to activate
	else
		display dialog "Don't start iTunes without LaCie external disk mounted." buttons {"OK"} default button 1 with title "Cannot start iTunes" with icon stop
	end if
end tell

Compile, save as script, add to dock, bingo. (Obviously, replace LaCie with the name of your external HD, as it appears in /Volumes when mounted.)

For extra points, you can give it iTunes’ icon too. Just get Info on iTunes and select the little icon in the top left (not the big one under Preview). Then just cmd-c, select the same icon in the script’s info window, and cmd-v.

This is fine in native desktop apps, but less fine in some text-mode programs (e.g. vim), when for some reason this often produces a superscript ³ instead.

So I’ve set up a custom keyboard mapping in iTerm to map F3 to #, which works nicely. However!

If I’m SSHed in to a remote Linux machine (or even my local Ubuntu VirtualBox) neither of these keys work in X apps. But, xmodmap (via the config file ~/.Xmodmap) can help. For some reason, Macs all have a dedicated key for these characters — § and ± — which no-one ever uses. But with this line in ~/.Xmodmap we can remap it to produce #:

keycode 18=numbersign

UPDATE: I’ve found a better way which works pretty much globally…

Using Ukelele you can copy the British keyboard layout and then remap keys to your heart’s content. I’ve moved the § character to the alt-§ key combination, in case I ever need it, and moved the # character to the raw § key. This seems to be respected almost everywhere so I don’t need to mess around with alt-3 or F3 any more. Joy. It also works over JollysFastVNC to a remote RealVNC server, which none of the other methods did.

Unfortunately, things still aren’t perfect. If I actually open a VirtualBox console session into GNOME on the local Ubuntu VM, the pointless § and ± key actually produces < and > so neither of these tricks work. In fact, I can’t get anything to generate a # even though I have the MacBook Pro Intl keyboard layout selected in GNOME. Any ideas?

UPDATE 2: YES!! I’ve finally cracked it for VirtualBox. With the help of the xkeycaps command, I discovered that X the keycodes coming into Ubuntu weren’t what I thought they were — somewhere the Mac-ness of the keyboard layout was getting lost. It turned out that the § key was generating keycode 94 instead. So I set up this in .Xmodmap on the Ubuntu VM:

keycode 94=numbersign

Now it works in VirtualBox too. Leave gifts of thanks below :-)

The first step is to install RasMol. There are various OS X ports out there — but I used the dead handy Fink to do this in one line:

fink install rasmol

However, RasMol is a Unix executable and not an application in the OS X sense, i.e. a .app file, which means you can’t select it as a download handler in Firefox. So, we need to wrap it in some AppleScript in order to allow this. The following AppleScript — my first :-) — gives you a RasMol Launcher ‘droplet’ which does the trick:

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-- flag to indicate whether script has been invoked as a droplet
set filecount to 0
 
-- run X11 if not running, then run RasMol (command shell and visualization window)
on run_rasmol(filename)
	do shell script "open /Applications/Utilities/X11.app; export DISPLAY=:0; /usr/X11R6/bin/xterm -e /sw/bin/rasmol " & filename & " &> /dev/null &"
end run_rasmol
 
-- open subroutine invoked by OS X if we run this as a droplet (i.e. file[s] supplied)
on open (filelist)
	repeat with filename in filelist
		set filecount to 1
		set filename to quoted form of POSIX path of filename
		run_rasmol(filename)
	end repeat
end open
 
-- if no files supplied (e.g. user double-clicked icon) run RasMol wih no params
if filecount < 1 then
	run_rasmol("")
end if

Click to download

This script starts X11 automatically, if it’s not already running, and for each PDB file dropped onto it, loads it into a separate RasMol instance (command prompt and visualization window). This kind of script is called a ‘droplet’, and can also handle being started from another application with one or more files supplied. If it’s just double-clicked, the on open subroutine is never called, and it opens a blank RasMol.

To create the script, open Script Editor — it’s in /Applications/AppleScript — paste in the source code, hit Compile, and save it as an application bundle called RasMol Launcher. This is a .app file which is really a directory containing the script and its metadata. Most OS X applications are bundled like this.

N.B. You may have to change /sw/bin/rasmol to wherever you installed it to, but this is the default Fink location.

Now, when you next click on a .pdb file in Firefox, you can choose your new RasMol Launcher droplet just like any application, and hit OK, and it should pop up just as if you’d double-clicked a local file. However, see the note about Firefox limitations below.

Associating .pdb files with RasMol Launcher in Finder

Because of the way OS X manages file associations, you can only associate .pdb files with the launcher droplet on a file-by-file basis to begin with (see this thread for why). This isn’t very helpful.

To fix this, we need to go into the bundle and edit some metadata. Go into the bundle in Finder by doing Show Package Contents (ctrl-click menu) and open Contents/Info.plist in a text or XML editor (or Property List Editor if you have the Apple developer tools). Find the CFBundleSignature key and change its string (should be dplt) to RSML. Then add a new entry underneath this with the key CFBundleIdentifier and the string uk.org.biotext.RasMolLauncher. Finally, open the Pkginfo file in the same folder, and change its contents to just the string APPLRSML.

After doing all this, you need to get OS X to re-read the application’s metadata — the quickest way is to move it to another folder, and back again. Now you should be able to Get Info on a .pdb file, change the application it opens with to RasMol Launcher, and click Change All to apply this to all .pdb files.

Firefox limitations

One quirk about Firefox — I think it’s a bug but Mozilla don’t — is that sometimes, the “do this automatically from now on” option when downloading a file doesn’t work. i.e. you can check it, but still get asked next time. The reason behind this is that some web servers are configured to serve files with the Content-disposition: attachment HTTP header, but don’t supply a specific MIME type. Instead they’ll have something like Content-Type: application/download.

In these instance, Firefox doesn’t consider it safe to open the file with the default app based on its filename extension alone, even if you asked for the automatic option before. So it pops the same dialogue box up again. Sadly, one of the sites that does this is pdb.org itself.

However, you don’t have to go all the way through the application selection process again. On my version of Firefox at least, assuming “Open with…” is selected, you can just hit OK and it’ll fire up RasMol Launcher again.