Setting Environment Variables for Sudo on Mac OS X

On Mac OS X you typically set up Unix environment variables in your ~/.bashrc or ~/.bash_profile files. To perform actions that need Root privileges you use 'sudo' instead of 'su'.

But when you 'sudo' a command your environment does not pick up your entire user environment and can cause problems in some cases.

To illustrate the issue, compare the output of these two commands in a Terminal (Unix shell):

$ printenv
$ sudo printenv

So how do you make a custom Environment variable visible to sudo? Rather than trying to modify system wide files like /etc/profile (which may not work anyway...) you want to modify the file /etc/sudoers.

Now, to modify this file you want to use the special command 'visudo', which as you can surmise, is a version of the editor 'vi'. Specifically it knows which file to edit and how to set the permissions on it. NOTE: If you don't know how to edit a file with 'vi' then learn the basics BEFORE you try the following steps!

$ sudo visudo

will bring the editor with the file opened. Look for this section:

# Defaults specification
Defaults        env_reset
Defaults        env_keep += "BLOCKSIZE"
Defaults        env_keep += "COLORFGBG COLORTERM"
[...]

The env_keep lines indicate that the named environment variable should be made available to sudo. So you want to add your custom variable to this list by adding lines like this at the end of this section:

Defaults        env_keep += "APXS2"

And I would suggest adding a comment line (preceded by a # character) that makes it clear that this is a custom change. Save the file and look at the output of sudo printenv:

$ sudo printenv
[...]
APXS2=/usr/sbin/apxs

Your custom environment variable should now be available.

 

Backtick operator in Jruby 1.5.3 not working

The backtick operator in Ruby (e.g. `date`) executes a system command.

In Jruby 1.5.3 this is not working and in my example caused some odd side effects. This is a known issue (http://jira.codehaus.org/browse/JRUBY-5133) that I'm sure will be fixed in the next release.

For now, use Jruby 1.4.1 as backticks seem to work fine here.


 

rvm on Mac OS X Snow Leopard

rvm, the Ruby Version Manager, is a great way to manage multiple Ruby versions. The documentation is extensive but I find it to be fragmented, such that if you do run into problems you have to look in multiple locations on the site to find relevant guidance.

On Mac OS X 10.6 (Snow Leopard) I had not problem installing rvm or ruby 1.9.2 but it blew up on my when I tried to list the gems under 1.9.2. The solution was to install zlib under the rvm tree:

$ ruby -v
ruby 1.8.7 (2009-06-12 patchlevel 174) [i686-darwin10.2.0]

$ rvm package install zlib
$ rvm install 1.9.2 -C --with-zlib-dir=$HOME/.rvm/usr

$ rvm use 1.9.2
$ gem list
$ gem install rails --pre

I had a similar problem when installing ruby 1.8.7 under rvm. This time it was the readline library that was the problem. Again, if you poke around in the docs you can find a fix:

$ rvm package install readline
$ rvm install 1.8.7 -C --with-readline-dir=$HOME/.rvm/usr

Although rvm makes it easy to switch back to your system ruby (with 'rvm system') I would strongly suggest that you do not use this. Instead, install the same release as your system ruby under rvm (1.8.7 in my case) and make that the default ('rvm --default 1.8.7').

You will have to reinstall gems under that ruby installation, which is a pain, but once you have all your rubies under rvm then you should have no issues with confusion over where specific libraries are located, which has been an issue for me more than once.

rvm also has a notion of gemsets, which I have not explored as yet, which allow you to isolate specific gem versions for specific applications. This could be extremely useful in migrating Rails applications to newer versions of Rails.

One area where I have not yet been successful is getting rvm and passenger to work. The rvm docs explain how to do this - but no luck for me as yet.


 

!! in Ruby

I noticed this odd looking construct in Rick Olsen's restful_authentication plugin a while back:

!!current_user

At face value it appears to be a 'double not' operation on the variable current_user. But that didn't make much sense to me at the time. I wondered if it was some special Ruby operator, but I could find no reference to it.

After a couple of experiments I see now that it is indeed a double not operator. It serves here as a very concise way to return true or false depending on whether the variable is nil or not. Here is how it works in an irb shell:

>> foo = nil
=>> nil
>> !foo
=>> true
>> !!foo
=>> false
>> foo = 1
=>> 1
>> !foo
=>> false
>>> !!foo
=>> true

Concise is good, but not at the cost of being unclear. I'm on the fence about this one.

 

Stripping non-ASCII characters from text in Ruby

I need to get rid of occasional non-ASCII characters in otherwise plain ASCII text, such as 'curly quotes' like “ and ”. I don't know the real encoding of my source text but I can tell that the characters are encoded as hexadecimal characters such as \x94

Here is the regular expression I use to remove them:

str.gsub!(/[\x80-\xff]/, '')

I'm sure this won't work in many cases but with my text it does the job just fine.



 

/etc/paths.d as a way to configure Paths in Mac OS X

Just found out about a simple way to manage paths to installed software in Mac OS X

As well as, or instead of, setting PATH environment variables in startup files, you can simply add a path as a file to the directory /etc/paths.d

For example, here is a command that sets up a path to a custom installation of MongoDB

$ sudo sh -c 'echo "/Users/jones/Documents/mypath/mongodb/bin" > /etc/paths.d/mongodb'

Start up a new shell and you will find that path added to your PATH environment variable.

Note that this is a system wide setting and so it gets set early in the process of shell creation. If you need to override PATH settings for specific users then you still need to set paths in .bashrc, etc. I don't know the order in which /etc/path.d files are sourced but I would assume alphabetical.

Also note that you need the 'sh -c ' construct in order to create the file as shown above. Simple 'sudo echo' will not work.


 

Mouse and Trackball Setup with MacPymol

I was having problems configuring a Kensington Expert Mouse Trackball to work correctly with the MacPymol protein modeling software on a Mac OS X 10.6.3 Intel Mac.

The Kensington mouse drivers (and specifically their MouseWorks software) has not been updated for several years and they are not supporting the trackball on Mac OS X Snow Leopard. But in fact the software works... MouseWorks is a 32bit version of a Preference Pane and so Preferences will have to shift to that version before you can interact with it.

But with just the trackball on that machine I was not able to configure the buttons correctly. That was the only mouse I had on that machine.

I noticed references in the MacPymol docs saying that the Apple Mighty Mouse with the little ball works well with the software. Even though I don't like that mouse, I did have one lying around so I plugged that it and configured it. With following setup it works as expected with MacPymol:

Left Button = Primary Button
Ball Button = Button 3
Right Button = Secondary Button

In 3-Button Viewing Mode this setup gives you Rotation on Left Button down and drag, Zoom on Right Button down and drag and XY translation on Ball Button down and drag.

Interestingly, once I had the Mighty Mouse setup like this, I could then get the Trackball working correctly. In Kensington MouseWOrks I have it set up as follows:
Left Lower button = Click
Right Lower Button = Right-Click
Left Upper Button = Middle-Click

MouseWorks knows about MacPymol (somehow) and you can setup MacPymol application settings - but I don't have this figured out. Unfortunately I'm not finding any more info in the MacPymol docs/wiki.

Hope this is useful