Redmine + Gitolite integration

I’m a big fan of both Redmine, the project management web application and Git, the distributed version control system.

Recently, I learned that it’s possible to integrate Git into Redmine so that git repositories for a project can be created via the Redmine web interface. This is done using plugins which connect Redmine with git hosting software: either gitosis or more recently, gitolite.

Unfortunately, this is a deeply-confusing process for novices like myself. There are multiple forks of the plugins, long threads in the Redmine forums that discuss various hacks/tweaks to make things work and no one authoritative source of documentation. After much experimentation, this is what worked for me. I can’t guarantee success for you.

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The “NoSQL” approach: struggling to see the benefits

Document-oriented data modeling is still young. The fact is, many more applications will need to be built on the document model before we can say anything definitive about best practices.
MongoDB Data Modeling and Rails

ismb2009.ff

ISMB 2009 feed, entries by date

This quote from the MongoDB website sums up, for me, the key problem in moving to a document-oriented, schema-free database: design. It’s easy to end up with a solution which resembles a relational database to the extent that you begin to wonder – if you should not just use a relational database. I’d like to illustrate by example.
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Getting your web application and R(Apache) to talk to each other

Here’s the situation. Web applications, built using a framework (e.g. Rails, Django) are great for fetching data from a database and rendering it. They’re not so great for crunching and charting the data. Conversely, R is great for crunching and charting, but doesn’t make for a great web application.

rapache-rails

Index view for values


The idea then, is to let each do what it does best and enable the passing of data between them. There isn’t a whole lot of literature on this topic, but there are a couple of guides:

  • In these seminar slides (PDF), Jeroen Ooms describes how data can be passed between a web browser and R. Briefly, he uses client-side javascript to format the data as a JSON string. Server-side R (RApache) then parses the POST variable using fromJSON() (in the rjson package), formats the results of an R function as JSON using toJSON() and sends them back to the browser.
  • Slide 46 of this presentation by Mike Driscoll of Dataspora illustrates a different approach, where a Django-based web application sends data to RApache in CSV format.

As a first step in understanding all of this, we can build a small demo application using Rails (version 2.3.5), which serves both JSON and CSV. We’ll see if we can get that into R, then see if R can return results back to Rails, via RApache. Baby steps, so we’ll avoid the AJAX stuff for now and just use Rails rendering methods to serve JSON from a controller.
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What I learned this week about: productivity, MongoDB and nginx

Productivity
It was an excellent week. It was also a week in which I payed much less attention than usual to Twitter and FriendFeed. Something to think about…

MongoDB
I’m now using MongoDB so frequently that I’d like the database server to start up on boot and stay running. There are 2 init scripts for Debian/Ubuntu in this Google Groups thread. I followed the instructions in the second post, with minor modifications to the script:

# I like to keep mongodb in /opt
PATH=/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/opt/mongodb/bin
DAEMON=/opt/mongodb/bin/mongod
# you don't need 'run' in these options
DAEMON_OPTS='--dbpath /data/db'
# I prefer lower-case name for the PID file
NAME=mongodb
# I think /data/db should be owned by the mongodb user
sudo chown -R mongodb /data/db
# don't forget to make script executable and update-rc.d
sudo /usr/sbin/update-rc.d mongodb defaults

nginx (and Rails and mod_rails)
This week, I deployed my first working Rails application to a remote server. It’s nothing fancy – just a database front-end that some colleagues need to access. I went from no knowledge to deployment in half a day, thanks largely to this article, describing how to make nginx work with Phusion Passenger.

Along the way, I encountered a common problem: how do you serve multiple applications, each living in a subdirectory?

# You have:
/var/www/rails/myapp1
/var/www/rails/myapp2
# You want these URLs to work:
http://my.server.name:8080/app1
http://my.server.name:8080/app2

Here’s how to do that:

# Make sure the Rails public/ directories are owned by the web server user:
sudo chown -R www-data.www-data /var/www/myapp1/public /var/www/myapp2/public
# Make symbolic links from public/ to the location which will be the web server document root
sudo ln -s /var/www/myapp1/public /var/www/rails/app1
sudo ln -s /var/www/myapp2/public /var/www/rails/app2
# These are the key lines in the server section of nginx.conf:
server {
        listen       8080;
        server_name  my.server.name;
        root /var/www/rails;
        passenger_enabled on;
        passenger_base_uri /app1;
        passenger_base_uri /app2;
}

That’s me for the week.

RSRuby and Rails revisited

A couple of months ago, I wrote a brief guide to displaying R plots in a Rails application using RSRuby.

It worked at the time – really it did – but since then, I’ve encountered problems. One is that despite sending the plot output to a PNG file, R X11 windows started to pop up on loading the web page containing the plot. Another is the appearance of long error messages related to “stack smashing” on terminating Mongrel server.

Fortunately, I read an excellent guide by Ana Nelson, R on Rails with RSRuby, which convinced me that I was doing things all wrong. So here is an amended version of my R + RSRuby + Rails “Hello World” application.
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