Installing PEAR packages through Composer

Did you know that you can obtain PEAR packages via Composer? And you don't need to install or set up PEAR or configure global settings!

A work colleague was talking about difficulties setting up CPAN for Perl on a server and that got me thinking about dependency managers and repositories and the options available in the PHP world. The modern way to manage dependencies and find libraries/packages is using Composer and Packagist but the old way was through using PEAR which was a global dependency manager with a repository of useful packages. I started to wonder if it was possible to load an old-style PEAR package through the new Composer dependency manager and after some fiddling about I got it working successfully.

Not long ago the PEAR guys decided to create a new version of PEAR so there are now two PEAR repositories available: classic PEAR (http://pear.php.net) and PEAR2 (http://pear2.php.net) which is also known as Pyrus. Most of the packages are still stuck in the old PEAR repository. So let's pick a test package from each of them to install. For PEAR2 I'm going to try the package suggested in the Composer documentation, PEAR2_HTTP_Request, and for old PEAR I'm going to try Numbers_Roman.

Open up the composer.json file and edit it so it looks something like this:

{
    "repositories": [
        {
            "type": "pear",
            "url": "http://pear.php.net"
        },
        {
            "type": "pear",
            "url": "http://pear2.php.net"
        }
    ],
    "require": {
        "pear-pear2/PEAR2_HTTP_Request": "*",
        "pear-pear/Numbers_Roman": "*"
    }
}

The two different PEAR repositories are defined in the repositories section of the composer.json file. Note the first two words (pear-pear and pear-pear2) used in the paths of the require values. This allows Composer to know which repository to look in. Details about choosing alternative channels are in the Composer documentation.

Then run php composer.phar update to install the new packages.

Now we can create a new PHP file to test the packages just installed. Here's my test code. Note that PEAR2 packages are namespaced, hence the use command:

<?php

require 'vendor/autoload.php';

use pear2\HTTP\Request,
    pear2\HTTP\Request\Adapter\Curl;

$url = 'http://www.yahoo.com/';
$request = new Request($url, new Curl());
$response = $request->sendRequest();

$nr = new Numbers_Roman();

//http response code 200 or 'CC' in roman numerals means success
if ('CC' == $nr->toNumeral($response->code)) {
    echo "Successfully accessed $url";
} else {
    echo "An error (HTTP{$response->code}) occured while trying to access $url";
}
?>

And that's it. Composer is just awesome!

Reading OBO Files in PHP using PhpObo

OBO files are specially formatted text-based human-readable files that contain ontologies, terms and descriptions, that describe a domain. At work I had a requirement to look through and double check the status of certain terms in the Mammalian Phenotype (MP) ontology. My first approach was to loop through the XML-based OWL format of the MP ontology, but I soon realised the OWL file was infrequently updated and I needed something much more current to work with. The other thing I noted was that other ontologies were not available in OWL format either, so what was really needed was a way to scan through the OBO files.

I had a little search and saw that there were solutions in Java and a Perl library but nothing in PHP, which is what my main application is written in so I decided to write my own OBO parser in PHP. Initially, it was going to be a really simple script to just loop through the OBO file but after reading the OBO format specification I realised I might as well write a proper library and set about writing PhpObo for myself and anyone else who would need it.

I have published the PhpObo library on Github under the Apache 2.0 license so feel free to use it, modify it and contribute if you wish. It is written in a flexible object oriented manner so you can swap out virtually any class from the library with your own version or extend its functionality. It is not a complete solution since it only works with one document at a time and doesn't resolve external ontology dependencies. But it does serve most people's needs and allow you to loop through any OBO file and it also allows you to generate your own OBO document using either an OOP or an Array-based (ArrayAccess) approach and serialize it out in the OBO file format.

If you wish to use PhpObo in your PHP 5.3+ project, I recommend you use a PHP PSR-0 dependency manager and autoloader like Composer to import the PhpObo project via Packagist.