hocuspokus.net

Copy/Paste Highlighted Code with Vim

2012-03-27T00:00:00+01:00

So, I’m preparing a presentation to give at work for one of our “brown bag” / “learning lunch” sessions and I want to put in some code into my slides…

When I used to use TextMate, I used the very cool copy as RTF bundle, for such tasks.

But now I’m a Vim head, here’s how to do the same in Vim…

First, install the highlight library (brew install highlight on the mac), then install the rtf-highlight Vim plugin^* – I recommend vundle to manage your plugins.

Now all you have to do is run the command :RTFHighlight <language> and the contents of your current buffer (or text selection) will be added to your clipboard as glorious syntax highlighted rich text, ready to paste into keynote etc! :)

^* You may need to apply the changes from this pull request to the Vim plugin to get it to work with more recent versions of the highlight library.

Brakeman

2012-03-07T00:00:00+00:00

Brakeman is an open source vulnerability scanner specifically designed for Ruby on Rails applications. It statically analyses Rails application code to find security issues at any stage of development.

Following this weekends Github hacking fiasco we’ve started running brakeman as part of our builds at work. Turned up some interesting things thus far – highly recommended!!!

There’s also a Jenkins plugin available to get nice graphs showing trends over time on your build pages – so go set that up too if you use Jenkins.

Easily Install Microsoft Internet Explorer Virtual Machines

2012-02-10T00:00:00+00:00

One of the guys at work found this yesterday – a nice automated install script to install the official Microsoft Internet Explorer testing virtual machines in Virtual Box on Mac OS X or Linux.

A geat tool for getting up and running to do IE testing!

When Using Apache As A Reverse Proxy To Passenger...

2012-01-31T00:00:00+00:00

ALWAYS remember to set:

ProxyPreserveHost on

Especially if you’re using the hostname to allow nginx to decide which passenger app to run – that was a few hours of my life wasted yesterday because of this…

Regexp Find and Replace in Ruby's gsub

2012-01-31T00:00:00+00:00

So I found this little trick quite useful the yesterday…

If you want to use a regular expression matched variable to find and replace sections of text in a string more intelligently (I used to do this all the time in Perl, hence why I was looking for a Ruby equivalent) you can!

Here’s a rather contrived example but it gets the message accross.

text = '<a href="#" class="button">click me</a><span class="weee">weee</span>'

puts text
# => <a href="#" class="button">click me</a><span class="weee">weee</span>

text.gsub!(/class="(.+)"/,'data-class="\1"')

puts text
# => <a href="#" data-class="button">click me</a><span data-class="weee">weee</span>

The Perl equivalent to \1 would be the $1 matched variable…

Sinon.js

2011-12-21T00:00:00+00:00

Standalone test spies, stubs and mocks for JavaScript. No dependencies, works with any unit testing framework.

Been using this at work lately in conjunction with QUnit – most useful!

The Black Art of BioMart: Ontology Searching

2011-04-19T00:00:00+01:00

We use BioMart a lot at my workplace, and one of the recent things I was tasked with doing was adding full ontology searching to one of our datasets – to be specific, MP ontology searching over some MP annotated phenotyping data. The desired functionality is so that a user can come in with an MP ID and retrieve any phenotyping data that has been annotated to that ID, or one of it’s children in the MP tree.

Time for a small disclaimer… ;–)

I’m not the first person to do this kind of stuff, it’s been about for a long time (GO searching has been in the Ensembl mart as long as I can remember), but i’ve never seen anyone write down how you do it. Also, please note that this info is for BioMart version 0.7 – the configuration mechanisms in the new 0.8 series are quite different (and i’ve not had a proper chance to play with 0.8 yet).

I’ve tried to document as much as I can but obviously when it comes to the XML examples you’ll have to take my code as a guide and apply the same principles to your datasets in MartEditor. Here we go…

The process boils down into the following tasks:

Set-up and configure an ontology dataset
- Create the (mp_ontology) staging table
- Populate the staging table with the required data
- Configure the (mp_ontology) dataset
Configure to our target dataset to use the ontology dataset

The Ontology Dataset

In order to enable full ontology searching, you must have a separate ontology dataset so that your target dataset (in my case the phenotyping data) can point into it. It’s a relatively simple single table BioMart dataset…

The Ontology Staging Table

The staging table for the ontology dataset takes the following form:

mysql> describe mp_ontology;
+-------------+--------------+------+-----+---------+-------+
| Field       | Type         | Null | Key | Default | Extra |
+-------------+--------------+------+-----+---------+-------+
| parent_id   | varchar(50)  | NO   | PRI | NULL    |       |
| parent_term | varchar(255) | NO   |     | NULL    |       |
| child_id    | varchar(50)  | NO   | PRI | NULL    |       |
| child_term  | varchar(255) | NO   |     | NULL    |       |
+-------------+--------------+------+-----+---------+-------+

Basically you fill it with mapping data for each parent ontology term. The data for each parent ID should include a mapping to itself, and all children below it e.g. for the root MP:00000001 there should be row where the child ID is also MP:00000001 and then rows for every single other MP term. It’s all a bit redundant, but this is what allows the mart to do the full ontology tree filtering.

Here’s a little script I knocked together to create and populate the mp_ontology table, it’s written in ruby, and uses the ols gem to get the ontology terms and ID’s (NOTE: you’ll need a local copy of the OLS database in order to use this script – more details are in the gem documentation).

#!/usr/bin/env ruby

require 'logger'
require 'optparse'
require 'ols'
require 'sequel'
require 'mysql2'

# Set the script options

@log        = Logger.new(STDOUT)
@log.level  = Logger::INFO
@debug      = false
@table_name = nil
@root_term  = nil

OptionParser.new do |opts|
  opts.banner = "Usage: build_ontology_table.rb [options]"
  opts.on("-d", "--debug", "Show debug output")                    { |d| @debug = d }
  opts.on("-t", "--table TABLE_NAME", "The table to create")       { |table| @table_name = table.to_sym }
  opts.on("-r", "--root_term ROOT_TERM", "The ontology root term") { |term| @root_term = term }
  opts.on_tail("-h", "--help", "Display help")                     { puts opts; exit; }
end.parse!

raise "You must define a --table to insert into!" if @table_name.nil?
raise "You must define a --root_term!"            if @root_term.nil?

# Connect to the BioMart database

@log.info("Connecting to BioMart staging database")
BIOMART_DB = Sequel.connect(
  :adapter  => 'mysql2',
  :host     => '127.0.0.1',
  :port     => 3306,
  :database => 'mart_staging',
  :user     => 'mart',
  :password => 'mart',
  :test     => true
)
BIOMART_DB.loggers << @log if @debug

# Now get on with stuff...

@log.info("Creating table '#{@table_name}' in staging database")

begin
  BIOMART_DB.drop_table(@table_name)
rescue
end

BIOMART_DB.create_table @table_name do
  String :parent_id, :size => 50, :null => false
  String :parent_term, :null => false
  String :child_id, :size => 50, :null => false
  String :child_term, :null => false
  primary_key [:parent_id,:child_id]
end

def insert_self( ont )
  ds = BIOMART_DB[@table_name].filter( :parent_id => ont.term, :child_id => ont.term )
  if ds.count == 0
    BIOMART_DB[@table_name].insert(
      :parent_id   => ont.term,
      :parent_term => ont.term_name,
      :child_id    => ont.term,
      :child_term  => ont.term_name
    )
  end
end

def insert_children( ont )
  terms      = ont.all_child_terms
  term_names = ont.all_child_names

  terms.each_index do |index|
    ds = BIOMART_DB[@table_name].filter( :parent_id => ont.term, :child_id => terms[index] )
    if ds.count == 0
      BIOMART_DB[@table_name].insert(
        :parent_id   => ont.term,
        :parent_term => ont.term_name,
        :child_id    => terms[index],
        :child_term  => term_names[index]
      )
    end
  end

  ont.children.each do |child|
    insert_self( child )
    insert_children( child ) if child.has_children?
  end
end

@log.info("Getting root term and building ontology tree")
tree = OLS::OntologyTerm.new(@root_term)
tree.build_tree

@log.info("Loading terms to staging table")
insert_self( tree )
insert_children( tree )

@log.info("Done. :)")

You run the script with the following options (just be warned, it takes a while for a large ontology):

ruby build_ontology_table.rb --table mp_ontology --root_term MP:0000001 --debug

Configuring the Ontology Dataset

Now that we have our ontology staging table, run through the normal MartBuilder process to setup and generate the SQL for creating your new mp_ontology dataset. (If you want to make the searches a touch more efficient, add indexes on the parent_id and parent_term fields whilst in MartBuilder). Before moving on run the build SQL to generate your dataset tables. Now, onto MartEditor.

In MartEditor we need to do the following:

Set-up filters for the parent_id and parent_term fields
Set-up an attribute for the child_id field
Set-up an exportable on the child_id attribute

Here’s my MartEditor XML (i’ll let you change the specific details for your means or click this through in MartEditor):

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE DatasetConfig>
<DatasetConfig dataset="mp_ontology" datasetID="13" displayName="Mammalian Phenotype (MP) Ontology" hideDisplay="true" interfaces="default" internalName="default" martUsers="default" modified="2011-04-19 10:06:02" softwareVersion="0.6" template="mp_ontology" type="TableSet" visible="0">
  <MainTable>mp_ontology__mp_ontology__main</MainTable>
  <Key>child_id_2010_key</Key>
  <Exportable attributes="child_mp_id" internalName="mp_id" linkName="mp_id" name="mp_id" type="link"/>
  <FilterPage displayName="FILTERS" internalName="filters">
    <FilterGroup displayName="FILTERS" internalName="filters">
      <FilterCollection displayName="mp ontology" internalName="mp_ontology">
        <FilterDescription displayName="MP ID" displayType="text" field="parent_id_2010_key" internalName="mp_id_display" key="child_id_2010_key" legal_qualifiers="=" qualifier="=" tableConstraint="main" type="text"/>
        <FilterDescription displayName="MP Term" displayType="text" field="parent_term_2010" internalName="mp_term" key="child_id_2010_key" legal_qualifiers="=" qualifier="=" tableConstraint="main" type="text"/>
      </FilterCollection>
    </FilterGroup>
  </FilterPage>
  <AttributePage displayName="ATTRIBUTES" internalName="attributes" outFormats="html,txt,csv,tsv,xls">
    <AttributeGroup displayName="FEATURES" internalName="features">
      <AttributeCollection displayName="mp ontology" internalName="mp_ontology">
        <AttributeDescription displayName="Parent ID" field="parent_id_2010_key" internalName="parent_mp_id" key="child_id_2010_key" maxLength="255" tableConstraint="main"/>
        <AttributeDescription displayName="Parent Term" field="parent_term_2010" internalName="parent_mp_term" key="child_id_2010_key" maxLength="255" tableConstraint="main"/>
        <AttributeDescription displayName="Child ID" field="child_id_2010_key" internalName="child_mp_id" key="child_id_2010_key" maxLength="255" tableConstraint="main"/>
        <AttributeDescription displayName="Child Term" field="child_term_2010" internalName="child_mp_term" key="child_id_2010_key" maxLength="255" tableConstraint="main"/>
      </AttributeCollection>
    </AttributeGroup>
  </AttributePage>
</DatasetConfig>

The main gist of it is this:

The filters are called:
- mp_id_display – this filters on the parent MP ID (NOTE: the ‘_display’ in the name is important – it’s to stop a name clash later on)
- mp_term – this filters on the parent MP Term
The important attribute is:
- child_mp_id – this returns on the Child MP ID’s
The exportable:
- is called mp_id
- points at the child_mp_id attribute

That’s the mp_ontology dataset configured we now need to configure our target dataset…

Configuring Our Target Dataset

The final step now is to configure the target dataset to use the ontology dataset for its ontology searches. So, what needs to be done is the following:

Add a hidden filter on the mp_id field that is already present in your dataset
Add an importable on tthis mp_id field – this will link it to the exportable in the ontology dataset
Add pointer filters to the mp_id_display and mp_term filters from the mp_ontology dataset

First up, the hidden filter… when I setup my example I created this in it’s own ‘FilterPage’ to separate from everything else in my config, (just in case I screwed things up) here’s the XML:

<FilterPage hideDisplay="true" internalName="mp_ontology">
  <FilterGroup hideDisplay="true" internalName="mp_ontology">
    <FilterCollection hideDisplay="true" internalName="param_level_heatmap_mp_id">
      <FilterDescription displayName="MP ID" displayType="text" field="mp_term" hideDisplay="true" internalName="param_level_heatmap_mp_id" key="id_1024_key" legal_qualifiers="=" qualifier="=" tableConstraint="phenotyping__param_level_heatmap__dm" type="text"/>
    </FilterCollection>
  </FilterGroup>
</FilterPage>

Then the importable:

<Importable filters="param_level_heatmap_mp_id" internalName="mp_id" linkName="mp_id" name="mp_id" type="link"/>

And finally the two pointer filters:

<FilterCollection displayName="MP ID" internalName="param_level_heatmap_mp_id_display">
  <FilterDescription displayName="MP ID" internalName="param_level_heatmap_mp_id_display" pointerDataset="mp_ontology" pointerFilter="mp_id_display" pointerInterface="default" tableConstraint="phenotyping__"/>
</FilterCollection>
<FilterCollection displayName="MP Term" internalName="param_level_heatmap_mp_term">
  <FilterDescription displayName="MP Term" internalName="param_level_heatmap_mp_term" pointerDataset="mp_ontology" pointerFilter="mp_term" pointerInterface="default" tableConstraint="phenotyping__"/>
</FilterCollection>

And that’s it – we now have MP searching! :)

Jack Daniel's Sauce

2011-03-04T00:00:00+00:00

It feels like this is turning into a food blog… lol!

Anyways, I’ve been wanting to make a Jack Daniel’s sauce for a long while, and after a bit of research on the interwebs and a little experimentation I settled on this simple recipe. It tastes fantastic as a dipping sauce or glaze with chicken, steak, shrimp and chips!

Ingredients

1/3 cup red onions, diced
¼ tsp garlic, crushed
½ cup water
½ cup molasses
1/3 cup teriyaki marinade
1/3 cup pineapple juice
½ cup jack daniel’s whisky
½ tsp tabasco sauce
3 tsp cornflour mixed with 3 tsp water

Directions

In a thick bottomed saucepan, gently fry the onions and garlic in a little olive oil until the onions start to soften.

Now add the rest of the ingredients except the cornflour mixture. Bring to the boil and gently simmer.

After about 35 minutes slowly add the cornflour mixture stirring constantly until the correct consistency is reached.

Use straight away whilst warm or you can keep it in a clean jam jar (or something like) in the fridge for a while.

IE6 Countdown

2011-03-04T00:00:00+00:00

10 years ago a browser was born. Its name was Internet Explorer 6. Now that we’re in 2011, in an era of modern web standards, it’s time to say goodbye.

MS, I salute you.

Yorkshire Puddings

2010-12-24T00:00:00+00:00

That’s the good deed done for today… :)

Pheasant and Mushroom Risotto

2010-12-15T00:00:00+00:00

I had some left over pheasant meat (breast and leg) to go with the stock that I made the other night, so I decided to make a nice risotto out if it. :)

The following quantities are for two servings.

Ingredients

Left over roast pheasant meat, cut into small pieces
2 large portobello mushrooms, sliced
6 dried porchini mushrooms
500ml pheasant stock
2 knobs of butter
1 tbsp olive oil
2 large shallots, finely chopped
1 clove of garlic, finely chopped
160g arborio rice
1 glass red wine
1 tsp dried mixed herbs
The juice of half a lemon
50g parmesan cheese

Directions

Rehydrate the porcini mushrooms in a little boiling water for 15 minutes. Remove the mushrooms and slice, then strain the leftover mushroom water and add to the pheasant stock.

Heat the stock. In a separate, heavy bottomed saucepan, gently sauté shallots and garlic in the olive oil and one knob of butter until soft.

Add the rice to the saucepan, turn up the heat and gently stir. After a minute or so the rice will become translucent. Now add the wine and keep stirring.

Once the wine has cooked into the rice add a ladle of hot stock, a good pinch of salt and the dried herbs. Now turn the heat down to a simmer and keep stirring gently.

Once the first ladle full of stock has been absorbed, add another one and keep stirring. Repeat this for about 10 minutes (stirring and adding stock).

Now add the pheasant meat and mushrooms to the saucepan, and carry on adding stock and stirring for a further 5 minutes. (So this will be about 15 minutes cooking time for the rice in total).

Now taste the rice to see if it’s cooked (also check the seasoning at this point). Carry on adding stock until the rice is soft but with a slight bite. If you run out of stock before the rice is cooked, add some boiling water and keep going.

Remove from the heat and add the last knob of butter and the parmesan, stir well. Place a lid on the saucepan and allow it to sit for 2 minutes – this allows the risotto to become all creamy and oozy like it should be.

Finally, add the lemon juice, stir, then serve immediately.

Pheasant Stock

2010-12-08T00:00:00+00:00

I made roast pheasant for the first time at the weekend (using this recipe – very nice!) so it meant that I ended up with the bones and carcasses from two pheasants. It would have been rude not to try and make a stock from them!

The following makes enough for about 4 servings.

Ingredients

2 pheasant carcasses and bones
3 tbsp vegetable oil
1 sliced medium onion
1 carrot – peeled, trimmed and sliced
1 celery stalk – trimmed and sliced
3 large shallots, sliced
2 tomatoes – coarsely chopped
4 bay leaves
4 juniper berries, crushed
20 peppercorns
2 ½ cup dry red wine
1 cup water or more

Directions

Preheat the oven to 450 °F / 230 °C / Gas Mark 8.

Pour the vegetable oil into a roasting pan with the reserved bones and carcasses. Roast until well browned, stirring occasionally, for about 30 minutes.

Add the remaining stock ingredients except the wine and continue to roast for 10 more minutes.

Transfer the solids to a stockpot, discarding any fat.

Place the roasting tin over high heat and add the wine. Scrape away all browned bits and boil, stirring, until the wine is nearly evaporated.

Add 1 cup of water, then add this liquid to the stockpot.

Add enough cold water to cover the bones and carcasses, bring slowly to a boil and skim well.

Lower the heat and gently simmer uncovered for 3 to 4 hours.

Strain, pressing down on the solids to extract all of the liquid, then the discard solids. Allow the stock to cool to room temperature and then refrigerate.

When the stock is chilled, lift off any solidified fat from the surface and discard.

Installing RMagick on Snow Leopard / Leopard

2010-03-06T00:00:00+00:00

This used to be quite a complicated task to install ImageMagick and RMagick from source, but these days (thanks to some great work by others) it’s a piece of cake…

First install ImageMagick using this install script hosted on github (http://github.com/masterkain/ImageMagick-sl):

cd ~/src
git clone git://github.com/masterkain/ImageMagick-sl.git
cd ImageMagick-sl
sh install_im.sh

Now simply sit back and wait. (Oh, you’ll need to enter your password at some points as the libraries are installed into /usr/local).

Then, once that’s done, RMagick is installed by:

gem install rmagick

Simples. :)

Installing the Ruby Bindings for Oracle on Mac OS X

2010-03-04T00:00:00+00:00

This quick crib sheet is for the guys at work (and anyone else who might need help on this one)…

First install the oracle instant client somewhere – I normally install it to /usr/local/oracle/instantclient_10_2. Then…

cd /usr/local/oracle/instantclient_10_2
ln -s libclntsh.dylib.10.1 libclntsh.dylib

Following this, run mkdir -p /usr/local/oracle/network/admin/, and place a copy of the tnsnames.ora file in this directory.

Now you need to add the following to your .profile or .bashrc file:

# Oracle env variables
export ORACLE_HOME="/usr/local/oracle/instantclient_10_2"
export DYLD_LIBRARY_PATH="/usr/local/oracle/instantclient_10_2:$DYLD_LIBRARY_PATH"
export SQLPATH="/usr/local/oracle/instantclient_10_2"
export TNS_ADMIN="/usr/local/oracle/network/admin"
export NLS_LANG="AMERICAN_AMERICA.UTF8"
export PATH="$PATH:$DYLD_LIBRARY_PATH"

That’s all of the set-up done, now you just need to install the gem:

gem install ruby-oci8

Done. :)

Removing ._ Files From Mounted Drives

2010-02-11T00:00:00+00:00

Here’s a quick snippet of goodness to remove those annoying ‘._’ files that Macs generate on mounted drives…

cd [wherever you want to clean]
find . -name "._*" -exec rm '{}' \; -print

Creating Users on a Linux System

2010-01-09T00:00:00+00:00

It’s been a while since I’ve had to do any basic sysadmin stuff on a Linux box… seeing as I had to google the answers to this I thought I’d better write them down!

useradd syntax

useradd [options] {username}

Useful options are:

-d – declare the users home directory
-m – force ‘useradd’ to create the home directory
-D – accept the system defaults for account settings

An alternative for ‘useradd’ though is ‘adduser’:

adduser {username}

This will then prompt you for all the information needed to set up the account.

making the user an administrator (with sudo)

As the root user…

visudo

Then underneath the entry for ‘root’ just add in an entry with the desired user name:

{username} ALL=(ALL) ALL

Git and Github

2010-01-04T00:00:00+00:00

Here’s the slides of another presentation I gave at work just before the Christmas break – this time on some of the development tools and resources that i’m using in my work: git and github.

The general gist is a basic introduction to both git and github, for developers who are already using version control (i.e. cvs or svn) but have yet to try distributed version control tools such as git.

Homebrew: The First Batch

2009-09-29T00:00:00+01:00

I’ve always fancied trying my hand at a bit of home brewing but never actually found the guts to get myself a kit. Well, this time I finally went through with it and I’m now the proud owner of a starter home brewing kit!

I got the kit from the folks at The Happy Brewer in Bedford, it was very reasonably priced, and they were very friendly and happy to explain what was needed to be done to a complete novice. If you live near the Bedford area and fancy having a go yourself I’d happily recommend them.

That there is potentially 40 pints of Woodfordes Wherry, a very tasty beer sold at the local near the Sanger Institute – fingers crossed I’ll do a good job of it. This is the first fermentation step, in about 4-6 days I can move it into the barrel, then it’s a 3-4 week wait for the finished product. Will update with news on whether I killed myself (and anyone else brave enough to try it) soon! :)

IWPLS 2009: The Sanger Mouse Resources Portal - a Testbed for Collaborative Data Integration

2009-09-21T00:00:00+01:00

Last week I enjoyed some time up in Edinburgh for the International Workshop on Portals for Life Sciences (IWPLS ‘09), hosted at the e-Science Institute. It was a good workshop – there were good presentations, lively debates, and good social planning for the evenings!

I have to admit that quite a lot of the content of the workshop was completely irrelevant to me and went straight over my head at times, but I did enjoy it, and it’s good to hear what other people are doing.

I was there for two reasons, first was an interest in the content of the workshop, and second was that I was one of the people presenting a lightning talk! The content of my talk was pretty different to most of the other presentations – they were mostly about grid computing and development of portal interfaces for said grids – whereas mine was about the architecture I developed for the new Sanger Mouse Resources Portal.

It seemed to go down pretty well, it got a couple of laughs, no one fell asleep and quite a few asked questions at the end, so I was quite happy at that. Here’s the slides from the talk, just in case anyone would like to take a look. Copies of all the presentations from the workshop can be found here.

My First Gem: Biomart

2009-08-31T00:00:00+01:00

A lot of my work these days involves building and querying biomart datasets. Interacting with the webservices (for queries) is pretty simple, you just have to post a piece of xml at the right url, but I found myself reusing a lot of boilerplate code in each and every new script.

So, to make my life a little easier (and hopefully some others) I packaged all of the code up in a module with classes to handle all of the monkey work for me and decided to release it as a gem. :)

The source code is available from github, and the documentation is on rdoc.info.

For more details, check out the release anouncement.

It’s my first ruby module so any advice or pointers on how to make things better would be most appreciated. :)

Add Git and SVN Branch to Bash Prompt

2009-07-09T00:00:00+01:00

EDIT: (12-Mar-2010) slight update to the svn prompt code to give a better / more useful output…

I’ve seen things like this posted on the net before but never really had a chance to play with the idea. But as I’m now using git and svn a lot more these days (fingers crossed i’ll be totally free of cvs soon!) I thought it was about time I pulled my finger out.

So here’s the end goal, in a normal directory, we just get a normal bash promt, but in a directory controlled by git or svn, we also get an addition telling us the source control tool in use and the current branch:

So, fire up yer terminal and add the following to your .profile, .bash_profile or .bashrc (whichever one you use):

parse_git_branch () {
  git name-rev HEAD 2> /dev/null | sed 's#HEAD\ \(.*\)# (git::\1)#'
}
parse_svn_branch() {
  parse_svn_url | sed -e 's#^'"$(parse_svn_repository_root)"'##g' | awk '{print " (svn::"$1")" }'
}
parse_svn_url() {
  svn info 2>/dev/null | sed -ne 's#^URL: ##p'
}
parse_svn_repository_root() {
  svn info 2>/dev/null | sed -ne 's#^Repository Root: ##p'
}

BLACK="\[\033[0;38m\]"
RED="\[\033[0;31m\]"
RED_BOLD="\[\033[01;31m\]"
BLUE="\[\033[01;34m\]"
GREEN="\[\033[0;32m\]"

export PS1="$BLACK[ \u@$RED\h $GREEN\w$RED_BOLD\$(parse_git_branch)\$(parse_svn_branch)$BLACK ] "

Simples. Now just open up a new terminal and move into a project directory using svn or git. :)

Building Apache and Mod Perl on Mac OS X

2009-03-07T00:00:00+00:00

I’ve finally had my work laptop upgraded to Leopard!!! :)

As such, I’ve just spent the last couple of days getting things all set-up nicely so that I can get on with my work. Most of the work that I do is web development orientated, and mainly using Perl and Catalyst, so an install of Apache and mod_perl is needed.

OS X does come with a complete install of Apache (even with mod_perl!) out of the box and ready to go (info on using this set-up can be found here), but I’m also working on another project that may involve the use of Jaxer, and this requires a newer build of Apache than the one shipped with Leopard. :(

Thankfully building these tools isn’t too complicated, here’s a quick dump of my notes on getting this done. Note, I’m installing them into /usr/local so that I don’t mess with any of the OS X internals that I shouldn’t be touching – this is completely removable.

First, make a work area for building:

sudo mkdir -p /usr/local/src
sudo chgrp admin /usr/local/src
sudo chmod -R 775 /usr/local/src
cd /usr/local/src

Apache

curl -O http://apache.mirror.infiniteconflict.com/httpd/httpd-2.2.11.tar.gz
tar zxvf httpd-2.2.11.tar.gz
cd httpd-2.2.11

Now here’s the big one – the Apache configuration. This compiles a heap of modules I probably don’t need, but it’s nice to have them there in case I do ever need them…

CFLAGS="-O3" CXXFLAGS="-O3" \
./configure --prefix=/usr/local/apache2 \
--enable-autoindex \
--enable-cache \
--enable-cgi \
--enable-deflate \
--enable-dir \
--enable-disk_cache \
--enable-fastcgi \
--enable-file_cache \
--enable-headers \
--enable-include \
--enable-info \
--enable-log_config \
--enable-log_forensic \
--enable-logio \
--enable-mem_cache \
--enable-mime \
--enable-mime_magic \
--enable-negotiation \
--enable-perl \
--enable-proxy \
--enable-proxy-balancer \
--enable-proxy-http \
--enable-rewrite \
--enable-speling \
--enable-status \
--enable-suexec \
--enable-userdir \
--enable-usertrack \
--enable-version \
--enable-vhost_alias \
--enable-so \
--enable-mods-shared=all

Then the standard make and install:

make
make test
sudo make install

Now to add some configuration so that Apache starts on system boot, first we need to create a startup script:

cd /System/Library/StartupItems/
sudo mkdir Apache
cd Apache
sudo touch Apache
sudo chmod a+x Apache
mate Apache

Paste this content into the file:

#!/bin/sh

##
# Apache HTTP Server
##

. /etc/rc.common

StartService () {
    ConsoleMessage "Starting Apache web server"
    /usr/local/apache2/bin/apachectl start
}

StopService () {
    ConsoleMessage "Stopping Apache web server"
    /usr/local/apache2/bin/apachectl stop
}

RestartService () {
    ConsoleMessage "Restarting Apache web server"
    /usr/local/apache2/bin/apachectl restart
}

RunService "$1"

Then a configuration file:

sudo touch StartupParameters.plist
mate StartupParameters.plist

Paste this content into the file:

{
  Description     = "Apache web server";
  Provides        = ("Web Server");
  Requires        = ("DirectoryServices");
  Uses            = ("Disks","Network Time");
  OrderPreference = "None";
}

Then reboot and open up http://localhost to make sure things have worked.

Mod Perl

This is a lot more straight forward:

cd /usr/local/src
curl -O http://perl.apache.org/dist/mod_perl-2.0-current.tar.gz
tar zxvf mod_perl-2.0-current.tar.gz
cd mod_perl-2.0.4
perl Makefile.PL MP_AP_PREFIX=/usr/local/apache2
make
make test
sudo make install

Now all you have to do is add the following line to your Apache httpd.conf (/usr/local/apache2/conf/httpd.conf) with all of the LoadModule entries:

LoadModule perl_module modules/mod_perl.so

All done! :)

Using Javascript to Make Relative Times Work with Caching

2009-02-05T00:00:00+00:00

A great idea from the folks over at 37 signals.

It’s easy to think that the relative-time style of this comment was written 15 minutes ago is incompatible with caching. How are you supposed to cache something if the text changes every minute? Static pages with JavaScripts, that’s how!

Update: Looks like this type of idea has been around for a while (I’d just never thought of it before)! :D

MS Announces Six Editions of Windows 7

2009-02-04T00:00:00+00:00

Should have expected this really. I would have thought producing all of these different versions of the OS would make development harder and more expensive – why not just produce one or two versions i.e. one for consumer and one for business use if you really need to segregate and fleece one market? Still at least it’s one different SKU down from Vista’s seven!

Microsoft has announced how it will package Windows Vista’s successor, Windows 7. And as ever, Microsoft has put segmentation ahead of clarity.

The one bright spot in Microsoft’s Windows 7 news is that – contrary to some reports – it won’t add a brand new edition solely for netbooks. Although even this is not that straight forward.

On Tuesday, the company Tuesday said Windows 7 would come in six editions: Windows 7 Starter Edition, Home Basic, Premium, Professional, Enterprise, and Ultimate.

Not that the news was presented like this. Microsoft led on the fact that “most” customers would be served by “two primary” editions – Windows 7 Home Premium and Windows 7 Professional that respectively target consumer and business users.

Want Git preinstalled on next Mac OS X?

2009-01-31T00:00:00+00:00

Yes would be my answer. It sounds like a good idea, but I’m not sure if Apple will appreciate the ticket spam though…

I have a dream where in the future developers don’t even have to install Git for themselves in order to be able to use it. Apple has shown a very forward thinking attitude towards shipping OS X with various programming languages and version control systems. Right now is a critical time in which we can help push to have Git preinstalled on the next version of their operating system. The more people that use Git, the better the ecosystem becomes, and removing the installation barrier is a big step in that direction.

I’m told, on good authority, that the best way to make this happen is to let Apple know that it’s something we desire. So if you’d like to be able to fire up a fresh Mac and type git without ever installing it, open a ticket on Apple’s bug reporting site:

http://bugreporter.apple.com

Let them know that you’re using Git on your mac, and that you’d love to see it shipped with the next version of OS X so that even more developers can experience the joy of distributed version control!

iPlayer Downloader Now on Mac and Linux

2008-12-18T00:00:00+00:00

This is good news! :)

The BBC has created a version of the iPlayer that works with both Mac and Linux computers.

The two systems, which have been able to stream BBC programmes via the iPlayer for a year, will now be able to handle downloads.

The BBC, working with Adobe, has developed the new version, known as BBC iPlayer Desktop.

Cloudcamb Notes: Biocep

2008-12-18T00:00:00+00:00

I went to an event called Cloudcamb last night (I love working in Cambridge) organised by Matt (ta very muchly), the evening was very good and informative, but the one thing that really stood out for me was a very interesting presentation on the Biocep project that anyone who uses R (or would like to use R) should be interested in.

Here’s my take on the basics of it and why you would want this – there’s really LOTS more there!!!

The first thing Biocep is (that’s not really advertised much on the site) is that it offers a vastly improved interface to R that has the following tools:

Built-in spreadsheet like functionallity
Built-in code editor (jEdit)
Plug-in architecture for creating custom interfaces to things (similar potential to Matlab’s GUIDE)

There are other R gui’s out there (i.e. Mac and Windows R spring to mind) – but they are not as slick as this.

The second thing biocep gives is that it allows you to run R instances on remote machines (i.e. up in the “cloud”, or on clusters or grid systems in your work place / institute), from your desktop and be able to work collaboratively with other people using fully shared sessions (i.e. both of you can play with shared data, talk and see all of the visuals the other person is seeing all in real-time – it’s really impressive to watch).

Seriously, if you work with R, check it out!

Buy My Book!

2008-11-26T00:00:00+00:00

Was I really involved in writing something that sounds this classy?!?!

Modern bioinformatics encompasses a broad and ever-changing range of activities involved with the management and analysis of data from molecular biology experiments. Despite the diversity of activities and applications, the basic methodology and core tools needed to tackle bioinformatics problems is common to many projects. Building Bioinformatics Solutions provides a comprehensive introduction to this methodology, explaining how to acquire and use the most popular development tools, how to apply them to build processing pipelines, and how to make the results available through visualisations and web-based services for deployment either locally or via the Internet. The main development tools covered in this book are the MySQL database management system, the Perl programming language, and the R language for statistical computing. These industry standard open source tools form the core of many bioinformatics projects, both in academia and industry. The methodologies introduced are platform independent, and all the examples that feature have been tested on Windows, Linux and Mac OS. This advanced textbook is suitable for graduate students and researchers in the life sciences who wish to automate analyses or create their own databases and web-based tools. No prior knowledge of software development is assumed. Having worked through the book, the reader should have the necessary core skills to develop computational solutions for their specific research programmes. The book will also help the reader overcome the inertia associated with penetrating this field, and provide them with the confidence and understanding required to go on to develop more advanced bioinformatics skills.

The book that I am a co-author on, Building Bioinformatics Solutions is shortly going to be available on

Amazon (UK)

and

Amazon (US)

as well as other countries.

If you’re looking for an introduction to some of the tools used in the field of Bioinformatics (programming, databases, data analysis) or even just looking for a general introduction to Perl programming, MySQL or R why not check it out. :)

Still here and after more?!?! Why not head on over to http://bixsolutions.net – the companion site for the book, and take a peek at what’s on offer.

Now get off my lawn! ;)

Using PostgreSQL with Ruby on Rails on OS X

2008-11-16T00:00:00+00:00

Following on from my last post for getting PostgreSQL up and running nicely on Mac OS X, my next task was getting it playing nicely with ruby on rails – I’m off on a rails course next week so I’m getting stuff ready. :)

It appears that there is currently two/three gem packages for using postgresql with ruby: postgres, ruby-pg, and pg – and from what I can make out, they’re all maintained by the same team now, (postgres was the original package, but it got abandoned – ruby-pg and pg are the replacements). As such, i’ll go with the newer ruby-pg gem…

sudo env ARCHFLAGS="-arch i386" gem install \
ruby-pg -- \
--with-pgsql-lib=/opt/local/lib/postgresql83 \
--with-pgsql-include=/opt/local/include/postgresql83

Then finally, when writing the database.yml entry for connecting to postgresql, we have to define our adapter as follows:

development:
  adapter: postgresql
  database: test_dev
  encoding: unicode
  host: localhost
  user: XXXXX
  password: XXXXX
  timeout: 5000

Install PostgreSQL on Mac OS X Leopard

2008-11-16T00:00:00+00:00

This type of guide is all over the internet, but I’m too lazy to search for one every time I want to do this. ;) So here’s a brief overview of how I got PostgreSQL set-up nicely on Mac OS 10.5…

Setting Up Our Environment

Using a text editor of your choice, add the following lines to the bottom of the /etc/profile file (you’ll need to be an administrator to do this):

# MacPorts
export PATH=/opt/local/bin:/opt/local/sbin:$PATH

# PostgreSQL
export PATH=/opt/local/lib/postgresql83/bin:$PATH

Now before we move on, make sure that you have MacPorts installed.

Installing PostgreSQL with MacPorts

I like MacPorts – it makes installing general Unix packages and keeping them up-to-date a snap. As such, we’ll use it to do the heavy lifting for installing PostgreSQL. Open up a terminal and hit up the following command:

sudo port install postgresql83 postgresql83-server

Sit back and wait a while… That’s the basic install done.

Now to configure it, do the following:

sudo mkdir -p /opt/local/var/db/postgresql83/defaultdb
sudo chown postgres:postgres /opt/local/var/db/postgresql83/defaultdb
sudo su postgres -c '/opt/local/lib/postgresql83/bin/initdb -D /opt/local/var/db/postgresql83/defaultdb'

This installs a default database instance for us to be getting on with. Next, run this command to get PostgreSQL to start on system boot:

sudo launchctl load -w /Library/LaunchDaemons/org.macports.postgresql83-server.plist

Reboot your Mac.

Creating a User Account and Database

Once your Mac is back up, we finally need to create an account for us to use (substitute ‘daz’ for your username)…

createuser --superuser daz -U postgres

Now a database to play with…

createdb test_db

Admin Your Database with pgAdmin 3

Download pgAdmin, then run the following commands to set up some functions that allows pgAdmin to collect statistics about your databases:

cd /opt/local/share/postgresql83/contrib/
sudo su postgres -c psql < adminpack.sql

That’s it – job done!

For notes on making the database accessible over the network, please refer to one of my posts on PostgreSQL on Ubuntu.

Sync Your Things Database via Dropbox

2008-11-06T00:00:00+00:00

Dropbox is a great service, I’m using it happily to keep my files in sync across multiple computers – I’m even using it to keep all of my passwords in sync, but I’ve thought of another great use… How about syncing my Things database between my macs (as this is my to-do list manager of choice)?

This is not fully tested yet, (just thought of it this morning) so i’ll update a bit later and report on as to wether things goes completely mental, but the way I’ve done this is as follows…

Make sure Things is completely shut down, then open up a terminal and type in the following commands:

cd ~/Library/Application\ Support/Cultured\ Code/

This moves us into the correct directory. First, to be on the safe side – we’ll take a backup of our files…

cp -R Things Things.bak

Now just move the Things directory into your dropbox and create a symbolic link in its place.

mv Things ~/Dropbox/
ln -s ~/Dropbox/Things Things

Fingers crossed this should have the desired results! :)

Update: It works!!! :D On the second computer all you need to do to get the ball rolling is to close down Things, open up a terminal and type the following commands:

cd ~/Library/Application\ Support/Cultured\ Code/
rm -rf Things
ln -s ~/Dropbox/Things Things

Note – my 2nd mac only had a fresh install of Things – no data. I installed it, opened it up (so the initial database was created), then did the above.

Gmail Gets Auto-Replies

2008-10-22T00:00:00+01:00

This is one feature that I’ve been wanting for ages!

Hello, you’ve reached Chad’s mailbox. Thanks for your email about the latest Labs feature: Canned Responses, or email for the truly lazy. I’m on paternity leave so I won’t be able to respond personally. Instead, I hope you’ll enjoy this automated message.

Android Goes Open Source

2008-10-22T00:00:00+01:00

Yesterday was a big day for advanced mobile phones – Android went fully open source.

I really like the iPhone (it will be my next phone) – it’s the most complete device out there, but I would love to see a truly open platform like Android have a great handset underneath it and really take off – it’s the only thing I can see that stands a chance of really taking on the iPhone. (Future unreleased editions of Windows mobile etc. don’t count – we’re looking at the here and now, these platforms won’t stand still while others try to catch up…)

Today is a big day for Android, the Open Handset Alliance, and the open-source community. All of the work that we’ve poured into the mobile platform is now officially available, for free, as the Android Open Source Project.

You’ll be hearing a lot about Android devices. We’ve all put a lot of effort into the first Android device, and I’m really happy with the way it turned out. But one device is just the beginning.

Android is not a single piece of hardware; it’s a complete, end-to-end software platform that can be adapted to work on any number of hardware configurations. Everything is there, from the bootloader all the way up to the applications. And with an Android device already on the market, it has proven that it has what it takes to truly compete in the mobile arena.

Blackbird - Javascript Logging Utility

2008-10-20T00:00:00+01:00

Found this while trawling the feeds this morning – looks like quite a useful utility. It offers a nice alternative to Firebug (when testing in browsers other than Firefox).

The Macalope: "Is This a Joke?"

2008-10-16T00:00:00+01:00

The Macalope bitch slapping some poor journalism – great reading.

Linux Now an Equal Flash Player

2008-10-16T00:00:00+01:00

Finally…

“As recently as 2007, Linux users waited six months for Flash 9 to arrive. Now, with Microsoft pushing its Silverlight alternative, Adobe is touting the universality of its Flash format, which has penetrated ‘98 percent of Internet-enabled desktops,’ it claims. And, it today released Flash 10 for Linux concurrently with other platforms. Welcome to the future.”

Wordpress Theme Notes

2008-10-13T00:00:00+01:00

I’ve been working on a theme for wordpress over the last few weeks (on and off), it turns out to be really quite simple, you just need to find out where to get started…

Here’s some pages that I found most useful (linking for future reference):

Ballmer in PCs Are Better Than Macs Shocker

2008-10-13T00:00:00+01:00

Ballmer goes on the defensive a shows just how ignorant he is… a great read! ;)

…you’ll see us be much more vigorous about stating the case for the PC. The truth of the matter is, this is ironic. The PC outsells the Mac 33 to 1. And despite the fact that we don’t sell PCs, we only sell Windows to people who make PCs. And the attack is actually on the PCs, interestingly enough. You’ll see us defend the PC. We’re going to talk about why — look, PCs are better than Macs. That is not something that can be debated. [TMO emphasis] 32 out of every 33 times, somebody buys a PC instead of a Mac. I’m not saying that there are not some things that people like about Macs, apparently there are. But have you ever seen a cheap Mac? No.

This one’s a great one too – has this guy even seen a mac in the last 10 years…

I’m very sensitive to exactly what mouse I have on my laptop. Can you find a range of choices? [for the Mac] Of course you can’t find a range of choices.

Release: toggleController Plugin 1.0

2008-10-04T00:00:00+01:00

I’ve just spent the last week on a Javascript and Ajax course (thanks to work for footing the bill)! As such I come armed with some newfound javascript knowledge! :)

Here’s the first fruits of my labour – a very simple jQuery plugin that enables you to unobtrusively make an element on a webpage collapsable, and have the showing/hiding controlled by another element.

Like I said, this is very basic stuff and there is probably about a million other (most likely more feature-full and better) plugins that do the same thing already on the web, but it’s all I really need for it to be useful for my stuff and I had fun learning how to do this – never know someone else may find it useful!

If you want to have a play, the code is on github.

Packard Bell looks to reposition self as 'trendy' lifestyle brand... LOL!

2008-09-23T00:00:00+01:00

Read this post and it just made me chuckle to myself…

Packard Bell is set to reposition itself as a trendy design-focused lifestyle brand, following its acquisition by Acer last year.

Speaking at Acer’s Global Press Conference, Emmanuel Fromont, Vice President of Packard Bell Sales and Marketing, said:

“It’s not a totally new positioning. We’ve always differentiated ourselves through design, but as a smaller company and having to do the design in-house, it was more difficult.”

“Now with Acer behind us, we want to create aficionado fans of our products. We want people to have real desire for our brand.”

Pocket-lint spoke to Acer UK country manager Bobby Watkins, and he told us that the new designs for Packard Bell were something we should look out for when they become available sometime next year.

Here’s what happened last time I saw a PB that was trying to be “trendy”:

Those things were a piece of crap, (and fuuuuugly) always falling apart and loads got returned… Let’s hope these are much improved – if not, it will always give us a laugh! :)

VMWare Fusion 2 is Out

2008-09-16T00:00:00+01:00

Go get it!

Great news for any virtualization junkies out there (I know I’m not the only one). VMWare Fusion 2.0 has just been released! Fusion 2.0 is a free upgrade for all existing 1.x customers, and it adds more than 100 new features and enhancements.

Google Adds Gears to Safari

2008-09-16T00:00:00+01:00

This is a worthwhile install if you’re a Wordpress user (or any other gears enabled system) on the mac – great to see some Safari lovin'. :)

We’re really excited to announce the official release of Gears for Safari on OS X (minimum requirements are Leopard 10.5.3 or Tiger 10.4.11).

You can download it today from http://gears.google.com.

This means that you can now access all the Gears-enabled sites (such as Zoho office, WordPress, the new YouTube uploader and Google Docs offline) in Safari.

eeeMac runs OS X on an eeePC

2008-09-12T00:00:00+01:00

I like…

I’ve heard some great things about the tiny little eeePC, but this is the best thing I’ve heard so far: it can be a Mac. Twitterer Gregory Cohen has pictures on Picasa of his completed eeeMac, an eeePC transformed (perhaps in similar fashion to this previous attempt — details please, Gregory) into an OS X-running ultraportable, complete with a tiny little lit Apple logo on the back.

History of the Browser User-Agent String

2008-09-11T00:00:00+01:00

I’ve only done user-agent string sniffing once and I remember it gave me a headache… This post explains why it gave me a headache! :(

And then Google built Chrome, and Chrome used Webkit, and it was like Safari, and wanted pages built for Safari, and so pretended to be Safari. And thus Chrome used WebKit, and pretended to be Safari, and WebKit pretended to be KHTML, and KHTML pretended to be Gecko, and all browsers pretended to be Mozilla, and Chrome called itself Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US) AppleWebKit/525.13 (KHTML, like Gecko) Chrome/0.2.149.27 Safari/525.13, and the user agent string was a complete mess, and near useless, and everyone pretended to be everyone else, and confusion abounded.

QGtkStyle now part of Qt

2008-09-10T00:00:00+01:00

Looks like KDE apps just got a whole lot more appealing to Gnome users. I like a lot of KDE apps (Kate being a particularly cool editor when I’m on the Linux box), but I just never used to use them much as they looked too out of place with the rest of my Gnome desktop (yeah, I guess I’m a GUI snob…) – this will most likely change that!

QGtkStyle made it’s way into the Qt snapshots this week, meaning it will become part of the Qt 4.5 release. Technical users can already compile and use it on their own desktop, but once Qt 4.5 is out it will simply replace Cleanlooks as the default application style Qt uses on GNOME desktops.

How Videogames Blind Us With Science

2008-09-10T00:00:00+01:00

An interesting article over at Wired discussing a recent study into how kids are using their brains and scientific reasoning to beat video games…

One of the reasons kids get bored by science is that too many teachers present it as a fusty collection of facts for memorization. This is precisely wrong. Science isn’t about facts. It’s about the quest for facts — the scientific method, the process by which we hash through confusing thickets of ignorance. It’s dynamic, argumentative, collaborative, competitive, filled with flashes of crazy excitement and hours of drudgework, and driven by ego: Our desire to be the one who figures it out, at least for now. It’s dramatic and nutty and fun.

And it’s pretty much how kids already approach the games they love. They’re already scientists; they already know the value of the scientific method. Teachers just need to talk to them in their language, so that the kids can begin to understand the joy of puzzling through the offline, “real” world too.

VMWare Fusion 2 Beta 2

2008-07-31T00:00:00+01:00

It’s got friggin' Unity for Linux!!! This looks good…

The VMWare team has just released the second beta for VMWare Fusion 2.0, the company’s popular virtualization program for the Mac.

The new beta adds a TON of new features, as the video above demonstrates. I got a chance to talk to VMWare today about the new beta and it is HOT. I’ll be posting a more in-depth overview tomorrow, but until then, here are some of the highlights:

Unity 2.0 – The newest version of Fusion is really focused on better Windows-Mac integration. You can now launch Windows programs from the dock or access Mac programs from within your virtual machine. You can also link folders like Documents, Pictures and Music on your virtual machine with those folders on your Mac.

Multiple Snapshots VMWare has worked really hard to bring a Time Machine-like ease to backing up and protecting your virtual machine. You can now designate how often you want to take full system snapshots of your VM, whether once an hour, once a day or once a week, and how many copies you want to keep.

Better Video and Graphics Graphics and shading support has been improved for Macs that have higher-end graphics cards, and even integrated Macs can now play 1080p HD video in virtual machines with considerably less CPU overhead.

Support for more client OSs, including Leopard Server You can now run Leopard Server as a VM in OS X 10.4 and 10.5, even on client machines (virtualizing Mac OS X client is blocked by Apple’s license terms). Support for the latest version of Ubuntu (Hardy Heron) is also available right out of the box with Unity integration. Power users can now designate up to four virtual CPUs per virtual machine, which is great for anyone wanting to take an XServe or Mac Pro to the next level.

VMWare Fusion 2.0 beta 2 is available for Intel Macs running OS X 10.4 or OS X 10.5. New users can try the beta for free and the upgrade path (including future betas and the full version of Fusion 2.0) is free for all existing Fusion 1.0 customers.

Gears of War 2 Introduces "Linked Achievements"

2008-07-29T00:00:00+01:00

Looks like people better get playing the original Gears leading up to November!!! (I know I will be… ;) )

Gears of War 2 will feature ‘linked Achievements,’ meaning that Achievements earned in the original Gears will help unlock bonuses in the sequel.

Epic’s Cliff Bleszinski took the stage at Comic-Con to demonstrate to a live audience the E3 Sinkhole level and describe a new “linked achievements” feature for Gears 2 where achievements unlocked in the first Gears game would open features in the upcoming sequel.

He offered three examples of how the system would work:

Complete Act One in Gears Of War and receive a playable Anthony Carmine in Gears of War 2

Find 10 COG tags in Gears Of War and get Minh Young Kim in Gears of War 2

Kill Raam in Gears Of War and earn a playable Raam in Gears of War 2

Questions such as whether all Gears of Wars achievements will be linked to the sequel and what other goodies can be grabbed besides characters won’t be answered until closer to the game’s November 7 release.

BBC working on New Tomorrow's World

2008-06-04T00:00:00+01:00

The BBC has announced that it is working on a successor to Tomorrow’s World. This was always one of my favourite shows as a child, (yeah, I know I’m a nerd ;) ), and I’m glad to see something like this making a return. We need some form of popular science show on TV, otherwise the vast majority of people will become ignorant of even the basics of science – but that’s a rant for another day…

Just a month after Sir David Attenborough said it was “very, very sad” that Tomorrow’s World had been axed – five years ago – the BBC has today revealed it is making a “new popular science format for the early evening” on BBC1.

A new science show is one of the BBC’s top priorities for BBC1 over the next year, according to its annual statements of programme policy for all its TV, radio and online services, published today. The SOPPs lay out the corporation’s programming plans for the year to the end of March 2009.

Trash Stuff From the Command Line

2008-05-26T00:00:00+01:00

A great little command-line tool for Leopard:

osx-trash manipulates the Mac OS X trash from the command line, just like the Finder does. It uses AppleScript via Scripting Bridge on top of to communicate with the Finder. You can move files to the trash, empty the trash, and list items currently in the trash.

Default Text Field Values That Disappear on Focus

2008-05-16T00:00:00+01:00

You will have noticed this effect out on your travels on the internet – a text input field has some default text in it (often in a slightly dimmed colour), and when you click on the text box, default text disappears and then reappears when you click away from the box. It happens on the search box to the right here too.

I needed this same effect at work today so a quick Google came up with this great blog post – a lovely example of the exact effect I was looking for in both raw javascript and a version using the jQuery library.

The script searches the page that it’s inserted on for all form input fields that have a class of ‘default-value’ applied. Each form input field must also have a unique ID.

When the page loads the script changes the color of the text in the text fields it has found to the value of ‘inactive_color’. If the user clicks on the input field, the default text is blanked, and the colour changed to ‘active_color’. If the user clicks away from the input field, i.e. the input field loses focus, the value of the text field will revert back to the original text, and the colour will change back to ‘inactive_color’, unless the user has entered some other text.

Here’s a copy of the jQuery version for my own personal notes, never know when that could be useful:

/*
 * Written by Rob Schmitt, The Web Developer's Blog
 * http://webdeveloper.beforeseven.com/
 */

var active_color = '#000'; // Colour of user provided text
var inactive_color = '#999'; // Colour of default text

$(document).ready(function() {
  $("input.default-value").css("color", inactive_color);
  var default_values = new Array();
  $("input.default-value").focus(function() {
    if (!default_values[this.id]) {
      default_values[this.id] = this.value;
    }
    if (this.value == default_values[this.id]) {
      this.value = '';
      this.style.color = active_color;
    }
    $(this).blur(function() {
      if (this.value == '') {
        this.style.color = inactive_color;
        this.value = default_values[this.id];
      }
    });
  });
});

However, we don’t use jQuery at work, our entire site is based around Prototype and script.aculo.us, so I did a bit of butchering and here’s the code adapted to use Prototype:

/*
 * Written by Darren Oakley
 * http://hocuspokus.net
 */

var active_color = '#000'; // Colour of user provided text
var inactive_color = '#999'; // Colour of default text

Event.observe( window, 'load', function () {
    var default_values = new Array();
    $$("input.default-value").each( function (s) {
        $(s).setStyle({ color: inactive_color });
        $(s).observe( 'focus', function () {
            if (!default_values[s.id]) {
                default_values[s.id] = s.value;
            }
            if (s.value == default_values[s.id]) {
                s.value = '';
                $(s).setStyle({ color: active_color });
            }
            $(s).observe( 'blur', function () {
                if (s.value == '') {
                    $(s).setStyle({ color: inactive_color });
                    s.value = default_values[s.id];
                }
            });
        });
    });
});

Now all you need to do is give your input text fields a unique id, and the class of ‘default-value’, then the script will take care of the rest.

Install PostgreSQL on Ubuntu 8.04

2008-05-13T00:00:00+01:00

Following up from my old guide to installing PostgreSQL (for Ubuntu 7.10), I thought i’d better do an update for the latest releases… :)

This quick walk-through are my notes for installing the PostgreSQL database server and the PgAdmin administration application on Ubuntu Linux, and also set up the server so it allows access to other PC’s on your network.

Before we move on, this guide was tested on the current release of Ubuntu Linux, (8.04 – Hardy Heron) and PostgreSQL 8.3, but it should also be applicable to older versions (of Ubuntu and PostgreSQL) and other Debian based distros.

Right for the basic installation, at the command-line, enter the following commands (or search for the listed packages in synaptic if you prefer that way of working):

sudo apt-get install postgresql postgresql-client postgresql-contrib
sudo apt-get install pgadmin3

This installs the database server/client, some extra utility scripts and the pgAdmin GUI application for working with the database.

Now we need to reset the password for the ‘postgres’ admin account for the server, so we can use this for all of the system administration tasks. Type the following at the command-line (substitute in the password you want to use for your administrator account):

sudo su postgres -c psql template1
template1=# ALTER USER postgres WITH PASSWORD 'password';
template1=# \q

That alters the password for within the database, now we need to do the same for the unix user ‘postgres’:

sudo passwd -d postgres
sudo su postgres -c passwd

Now enter the same password that you used previously.

Then, from here on in we can use both pgAdmin and command-line access (as the postgres user) to run the database server. But before you jump into pgAdmin we should set-up the PostgreSQL admin pack that enables better logging and monitoring within pgAdmin. Run the following at the command-line:

sudo su postgres -c psql < /usr/share/postgresql/8.3/contrib/adminpack.sql

Finally, we need to open up the server so that we can access and use it remotely – unless you only want to access the database on the local machine. To do this, first, we need to edit the postgresql.conf file:

sudo gedit /etc/postgresql/8.3/main/postgresql.conf

Now, to edit a couple of lines in the ‘Connections and Authentication’ section…

Change the line:

#listen_addresses = 'localhost'

listen_addresses = '*'

and also change the line:

#password_encryption = on

password_encryption = on

Then save the file and close gedit.

Now for the final step, we must define who can access the server. This is all done using the pg_hba.conf file. (The following advice can also be given to you – plus you don’t even need to figure out IP addresses and subnet masks – from the latest versions of pgAdmin (1.6.x). But it doesn’t hurt to know how things work).

sudo gedit /etc/postgresql/8.3/main/pg_hba.conf

Comment out, or delete the current contents of the file, then add this text to the bottom of the file:

# DO NOT DISABLE!
# If you change this first entry you will need to make sure that the
# database
# super user can access the database using some other method.
# Noninteractive
# access to all databases is required during automatic maintenance
# (autovacuum, daily cronjob, replication, and similar tasks).
#
# Database administrative login by UNIX sockets
local   all         postgres                          ident sameuser
# TYPE  DATABASE    USER        CIDR-ADDRESS          METHOD

# "local" is for Unix domain socket connections only
local   all         all                               md5
# IPv4 local connections:
host    all         all         127.0.0.1/32          md5
# IPv6 local connections:
host    all         all         ::1/128               md5

# Connections for all PCs on the subnet
#
# TYPE DATABASE USER IP-ADDRESS IP-MASK METHOD
host    all         all         [ip address]          [subnet mask]  md5

and in the last line, add in your subnet mask (i.e. 255.255.255.0) and the IP address of the machine that you would like to access your server (i.e. 138.250.192.115). However, if you would like to enable access to a range of IP addresses, just substitute the last number for a zero and all machines within that range will be allowed access (i.e. 138.250.192.0 would allow all machines with an IP address 138.250.192.x to use the database server).

That’s it, now all you have to do is restart the server:

sudo /etc/init.d/postgresql-8.3 restart

And all should be working.

First Gears of War 2 Footage

2008-05-12T00:00:00+01:00

Time to get that pre-order on, this looks like it’s going to be awesome…

Orb - Live TV on iPhone

2008-05-08T00:00:00+01:00

That’s it, I REALLY want an iPhone now…

You don’t need Steve Jobs' permission to watch TV on your iPhone any more. And you don’t need to pay the cable company twice. A native Orb client for the iPhone and iPod Touch popped up on the installer networks overnight, and Orb confirms that it’s official.

The client software allows you to watch live TV on an iPhone or Touch wherever you are, in addition to your music. You’ll need a TV card or adaptor for your PC, of course, to get the live TV. So provided you have an internet connection, there’s no need to perform DIY transcoding using software such as Visual Hub. The client will even transcode the video stream nicely for 2.75G Edge networks. Orb does in software what Sling Media does in hardware.

What Do You Do With Old Versions of IE?

2008-05-07T00:00:00+01:00

Was round the in-laws the other day and couldn’t help but notice this one in the garden…

A fine way to retire an old web browser. At least it’s found some use… :D

Installing R/BioConductor on Ubuntu 8.04

2008-05-07T00:00:00+01:00

The new version of Ubuntu is out, (as if you haven’t heard that by now), so that means a fresh install to play about with and working just the way I want! :D

One of the tools that I currently need (for the thesis work) is R and the BioConductor libraries. So here’s a quick run down on getting them up and installed on Hardy…

First up, run these commands in a terminal:

sudo apt-get install build-essential g77 gfortran
sudo apt-get install refblas3 refblas3-dev zlib1g-dev
sudo apt-get install r-base

This will then install the R base packages and some of the BioConductor packages, along with the gcc and fortran compilers and some other libraries that will be required for the next step.

sudo -s
R

Now at the R prompt, type the followingâ€¦

source("http://www.bioconductor.org/biocLite.R")
biocLite()

Now sit back for a few minutes while your system configures BioConductor for you.

If Browsers Were Women...

2008-05-07T00:00:00+01:00

Installing VMware Tools on Ubuntu 8.04 (Hardy)

2008-05-05T00:00:00+01:00

If you’re a VMware user and want to play around with the latest version of Ubuntu in a VM (like me), you’ll need to get the vmware-tools installed. Unfortunately, things are not quite as straight forward as the previous release of Ubuntu yet, but it was a pretty easy thanks to this great guide.

The latest version of Ubuntu (8.04 a.k.a. Ubuntu Hardy – the world’s most popular Linux distribution) came out yesterday on April 24th. I downloaded it right away to play with on VMware Fusion, my Mac virtualization tool of choice (though I’ve now been told this works in VMware Workstation and VMware Player on the PC too!). It worked pretty well out of the box, with even seamless mouse support working right away, but I needed, of course, to install VMware Tools too, as any good VMware user would do. From there, things turned sour, and I was bombarded with error messages …

Spanning Sync 2.0 to Add Contact Sync

2008-04-22T00:00:00+01:00

I’m already a lover of Spanning Sync, version 2 promises to have contact syncing between all your Google apps with the Mac address book. This could be very very good. Check the link for a video of it in action.

People know Spanning Sync for its ability to sync Apple iCal with Google Calendar. In fact, more than 70,000 people have used Spanning Sync to do just that. But calendars are only one part of the equation.

Our users tell us that they also need to be able to sync their Mac Address Book with their contacts in Gmail and Google Apps. So Spanning Sync 2.0 does both calendars and contacts.

AVG Free Gets an Update

2008-04-22T00:00:00+01:00

If you, like most of the world, are a Windows user, having to run things such as anti-virus and anti-spyware programs are just a part of everyday life to try and keep your system running nicely.

My personal favorite, that I install on all the Windows PCs that I regularly have to keep in check (family, friends who haven’t seen the light of Mac or Linux etc.) is AVG. Great news is that AVG plan to release the new free edition of AVG 8.0 on Thursday now with added spyware protection to boot! Great news, and sounds like it could be an essential upgrade.

AVG Technologies plans to release a revamped version of its popular, free anti-malware scanner on Thursday.

Version 8.0 of the software will add anti-spyware and safe search features to its core anti-virus engine. Safe surfing features, that give users warnings about visiting insecure websites all the time not just when they search, will remain a paid feature of AVG’s full fat product.

Both the safe search and safe surfing features use Linkscanner technology, acquired by AVG when it bought Exploit Prevention Labs last December

Some People Have Waaay Too Much Time...

2008-04-21T00:00:00+01:00

This is one way to get your perfect coffee fix…

If you’re both a coffee and gadget freak, this project by DIY'er Tim Hirzel will probably be a notably inspiring hack. By combining a fancy-pants Rancilio Silvia espresso machine, the multi-purpose Arduino micro-controller, a Wii nunchuk, and some seriously high-level hacking, Tim has created a one-of-a-kind masterpiece. The typically straight-up espresso maker is now controlled electronically, allowing integration of a calendar, sleep timer, wake-up alarm, and temperature regulation. The system also allows a user to time its functions (to get that perfect cup of espresso), and the nunchuk can be used to alter settings on the unit. Be sure and take a look at the video after the break to see this mod in action.

Open Sauce?

2008-04-16T00:00:00+01:00

Okay, really bad pun…

Just come across this website Open Source Food. It’s yet another social networking site, but the difference with this one is that it is centered around one of my favorite things – Food!

Should be well worth a look for a few interesting recipes.

Amazing Recipes. Delicious Food. Beautiful Photography. Created and rated by you and fellow food-lovers from all over the world. Open Source Food is your gastronomic hub where every visit will bring inspiration and a rumbling belly…

Fring for iPhone

2008-04-16T00:00:00+01:00

Dan in the office has Fring on his Nokia and it seems pretty cool – this looks quite useful, let’s just hope the call quality gets improved though (3G should help this out).

Sure, the iPhone is cool looking, works out a lot, and is really good at math… but it can’t do VoIP, can it? Well, yes it can — and you can, thanks to a company called Fring and a piece of ingenious software (for jailbreakers only). Using the native app, it’s now possible to place and receive calls via your WiFi connection, thus making AT&T CEOs cry like little babies. Besides doing Skype and the like, the app also lets you connect for chats via MSN Messenger, ICQ, GTalk, SIP, Twitter, AIM, and Yahoo!, which should make this an attractive package even if you don’t want to harness the raw power of IP telephony. You can get the application for free by loading up Installer with the company’s repo. Check the video after the break to see the magic happen.

Check out the link for a video of it in action.

iPhone £100 Cheaper? Yes Please!

2008-04-15T00:00:00+01:00

Ohh, now the question is – do we wait for the 3G version or not… (I think this – if it is true – is a pretty good sign that the 3G version is around the corner).

O2 will cut £100 off the price of the Apple iPhone tomorrow, it has been claimed. Carphone Warehouse is said to be planning to match the move.

There’s no official confirmation yet, of course. The claim was made today by website Mobile Today.

If O2 and CW do knock £100 off the price of the iPhone, taking the handset’s price to £169, it will undoubtedly further fuel speculation that carriers are clearing out stocks of the 2.5G phone ahead of the widely anticipated introduction of a 3G version in June.

COD4 is Awesome!

2008-04-13T00:00:00+01:00

Late to the game as always, I finally got onto COD4 last night.

Oh. my. god. This game is frigging awesome!

I had no idea what I was doing half the time, and spent most of the night watching replays of how I died, but I haven’t had a laugh like this with a game since Gears of War came out. Halo 3 was good, great even – but it just didn’t have that stand out ‘you’re gonna remember this’ feeling to it, it was just more, well, Halo.

Maybe this is because COD4 is my first COD game and i’ve just been missing out all of these years (the WWII stuff never really appealed).

Anyway, enough of my rambling… If you own a machine capable of gaming in anyway, be it Xbox, PS3, Wii, PC, your toaster, whatever – you need to try out COD4.

Oh, and for real giggles, try an 18 player free-for-all on the world’s smallest map ‘Shipment’. I think I had on average about 5 seconds between respawns! :D

Quake 3 for the iPod Touch/iPhone

2008-04-11T00:00:00+01:00

I somehow managed to miss this one. Quake 3 running on hacked iPod Touch’s! They keep making it harder and harder to resist an iPhone/iPod Touch…

Future generations will most likely divide the timeline of history at this point: when Quake 3 achieved motion-sensing, wireless network play on two iPod touches. Just think, less than a year ago we were salivating (or at least mildly enthused) at the prospect of rocking Doom on this thing, and now Quake 3 Arena is yours for the taking — or at least will be once we get any sort of hard info on this app.

London Teen Orders 'cab, innit'

2008-04-11T00:00:00+01:00

This made me chuckle so much I had to link to it! Omgi’s need to be stopped… ;)

A 19-year-old Saaarf London girl has been advised to use the Queen’s English on the phone after her hunt for a cab to whisk her to Bristol airport ended less than satisfactorily.

According to the Daily Mail, the unnamed teen rang directory enquiries two weeks ago and initially requested a number for a “Joe Baxi” firm. The nonplussed operator told her she couldn’t find anyone by that name, to which the lass replied: “It ain’t a person, it’s a cab, innit.”

The enlightened operator duly put her through to Bishop’s Stortford-based retail display supplier Displaysense, where she “spoke to an equally bemused saleswoman” before thundering: “Look love, how hard is it? All I want is your cheapest cab, innit. I need it for 10am. How much is it?”

The answer was £180, and with the deal done by credit card, Displaysense obliged by delivering a display cabinet to her door the next morning.

10 Ways to Instantly DEcrease Productivity on your Mac

2008-04-02T00:00:00+01:00

A great guide to help you in not getting things done. :D

Sure, we’ve all read those lists of tweaks you can make to your system to increase productivity, but what if you’re not in such an all-fired hurry to get things done? What if you’re already plenty efficient, and actually need to slow things down a bit until that five o'clock whistle blows? Well, lucky for you, we’ve compiled a list of the top ten best ways to slow down your system, and decrease productivity. Please feel free to add your favorites in the comments. (Oh, and we by no means recommend you do any of these to your friends' computers, even if it IS April 1st).

Unix Toolbox

2008-03-23T00:00:00+00:00

Found this via a post on Digg. A very useful read if you want to get some more advanced things done in Unix.

This document is a collection of Unix/Linux/BSD commands and tasks which are useful for IT work or for advanced users. This is a practical guide with concise explanations, however the reader is supposed to know what s/he is doing.

Developing Rails Applications on Mac OS X Leopard

2008-03-16T00:00:00+00:00

First in a series of three articles from Apple on Ruby on Rails development on Mac OS X Leopard. Definitely worth a bookmark.

Ruby on Rails is a popular and powerful open source web framework for rapidly creating high-quality web applications to help you keep up with the speed of the Web. Rails is thriving on Mac OS X, and Leopard comes pre-installed with Ruby, Rails, Mongrel, Capistrano, Subversion, and other tools that help to streamline the development and deployment of Rails applications. In addition, the Organizer feature of XCode 3.0 keeps your development workflow efficient.

This article gives you a full tour of Ruby on Rails 2.0 on Leopardâ€”starting with building a web application using the latest Rails features with Xcode 3.0, and finishing with deploying the application to a production server running Leopard Server. Along the way we’ll explore unique features and benefits that Leopard brings to the party. In the end you’ll be better equipped to consider the advantages of powering your web application with Rails on Leopard.

This is the first in a series of three articles:

This article on Development, where you learn to build a basic RESTful Rails application using Xcode 3.0;

Customization, where we discuss working with views and web forms, adding AJAX support, and supporting an iPhone interface;

Deployment, where we set up version control, write a Capistrano recipe, and deploy on Leopard Server.

Together they will give you a great start in working with Rails on Mac OS X Leopard.

IE8 Will Be Standards-Compliant By Default

2008-03-08T00:00:00+00:00

I have to say that I’m quite surprised at this u-turn, but hell it’s great news! :)

We’ve decided that IE8 will, by default, interpret web content in the most standards compliant way it can. This decision is a change from what we’ve posted previously.

Bio-Linux - Bioinformatics Tools for Linux

2008-03-07T00:00:00+00:00

Bio-Linux is a specialised Linux disro that provides both standard and cutting edge bioinformatics software tools on a Linux base.

I wrote a post on my old blog a little while back now detailing how to use the packages from Bio-Linux in Ubuntu Linux, but it got missed in the migration (sorry to all those who have been searching for it). Here’s a repost and update for Ubuntu 7.10…

Log into your system and open up a terminal, then follow these steps:

sudo gedit /etc/apt/sources.list

Add the following lines to the end of the file:

# Bio-Linux package repository
deb http://envgen.nox.ac.uk/bio-linux/ unstable bio-linux

Save and close the file, now back at the terminal type the following (Note that we need to install the bio-linux-staden package, without this we’d have to do a bit more hacking in config files to stop getting errors whenever we open up a terminal):

sudo apt-get update
sudo apt-get install bio-linux-base-directories bio-linux-staden

Next step is to set-up your environment for Bio-Linux…

sudo gedit /etc/bash.bashrc

Add the following lines to the end of the file:

# Set up Bio-Linux Environment
source /usr/local/bioinf/config_files/aliasrc
source /usr/local/bioinf/config_files/bioenvrc

Save and close the file.

That’s it, now all of the packages available through Bio-Linux are now available to you in Ubuntu. One final word of warning… I’ve noticed that a few of the packages are a little out of date, (the Bio-Linux version of Taverna is 1.4, but 1.7 is now available) so it might be worth checking the version numbers before installing things.

The other thing to note with the Bio-Linux version of Taverna – it doesn’t start properly without a little bit of hacking… :( (If you decided to go with the Bio-Linux version, you can launch it by running the following in the terminal: /usr/local/bioinf/taverna/taverna/runme.sh).

Oh god, 8 is on the way...

2008-02-25T00:00:00+00:00

Hold onto your hats people, it looks like Microsoft is getting IE8 somewhere near usable. It’s started a private beta test already with a public one set to follow… Let’s hope they do a u-turn on this stupid version meta tag and have the damn thing render in “super-standards” mode from the outset.

Microsoft has sent out invitations to a select number of testers allowing them to participate in a “limited technical beta program” for the upcoming Internet Explorer 8. The announcement also says that there will be a public beta as well, once the invitation version is complete.

So far we know that Microsoft claims that IE 8 will pass the ACID 2 compatibility test and include support for a controversial version tag, which will allow web developers to force the browser into “super-standards mode” enabling the browser to correctly render webpages that adhere to the W3C’s standards.

We’ve written before about the contentious debate surrounding the so-called version tag, but the basic idea is that website developers will be able to add a meta tag to their pages telling IE how it should render the page in traditional mode (non-standard IE 6-style rendering), standards mode (IE 7’s half-baked concept of standards) and super standards mode (where IE will render similar to the way Firefox, Opera and Safari have been doing for the last five years).

A number of developers have decried the meta-tag flagging as a way of versioning the web, which they feel is a bad idea. But regardless of how the meta-tag might play out, we find it interesting that, if the rumors are to be believed, IE 8 will automatically render in traditional mode.

Gears of War 2 - November

2008-02-21T00:00:00+00:00

This has officially just made my day! :D

Microsoft has officially announced that the Xbox 360 sequel to the popular shooter Gears of War will launch in November of this year.

Much of the Xbox 360’s first year success was dependent on Epic’s Gears of War. It proved much more than just substitute until Halo 3 arrived and really showed the gaming quality that the console could deliver. In fact, many still favour Marcus Fenix over Master Chief Petty Officer John-117.

UK ISPs To Start Tracking Your Surfing To Serve You Ads

2008-02-19T00:00:00+00:00

Don’t the ISP’s already have a revenue stream?!? I mean I do pay for my internet connection, why on earth would they think that i’d like adverts shoved down my throat as well! O2/Be – you better not be looking into this…

TechDirt has an interesting article about a UK-based company that is trying to work with ISPs to make use of user surfing data to serve targeted ads. “Late last year, we heard about a company that was trying to work with ISPs to make use of that data themselves to insert their own ads based on your surfing history — and now we’ve got the first report of some big ISPs moving into this realm. Over in the UK three big ISPs, BT, Carphone Warehouse and Virgin Media have announced plans to use your clickstream data to insert relevant ads as you surf through a new startup called Phorm.”

R.I.P. HD DVD

2008-02-19T00:00:00+00:00

Boy am I glad I didn’t buy that HD DVD player for my Xbox 360… :)

Toshiba has abandoned HD DVD “following recent major changes in the market”, it announced this morning. The company spun the failure of its favourite format as a move made to strengthen the industry.

The consumer electronics giant said it will “no longer develop, manufacture and market HD DVD players and recorders”.

It will begin to reduce shipments of HD DVD players to retail channels, aiming to stop shipping product by the end of March.

HP 2133 UMPC

2008-02-19T00:00:00+00:00

Engadget are running a story with pics for HP’s answer to the Eee PC. It does look quite sweet, but no details of the full spec or final price as yet.

If they could pitch this about the same price as the Eee – I could see this being quite sweet… However, it says that it can come with Vista or Linux – my bet is that it’s going to be a touch more powerful than the Eee (it’ll need to be if Vista is an option!), and a shedload more cash!!! Please let me be wrong, (on the cash point ;) )!

How to Fix Microsoft's Browser Issues

2008-02-19T00:00:00+00:00

Hakon Wium Lie (CTO of Opera):

In the area of web browsers, Opera Software has proposed a specific kind of remedy – that Microsoft only be allowed to distribute standards-compliant browsers. Microsoft’s IE is bug-ridden and the company, despite its vast resources, has shown little interest in fixing problems that cost web designers time and sleep. IE dominates the web due to its being bundled with Windows. This forces web designers to prioritize coding for IE. Coding for standards-compliant browsers becomes a secondary consideration.

Microsoft is keenly aware of this and therefore has little interest in improving their support for standards. They will never become standards compliant unless forced by someone in a position to demand a change, something that users and customers are not. Requiring standard compliance would greatly lessen Microsoft’s monopolistic stranglehold in the web browser market, would delight web developers everywhere and would, ironically, make IE a better product.

He’s a fan of Microsoft’s latest proposals in conjunction with IE8…

Breakdown of Modern Web Design

2008-02-19T00:00:00+00:00

Found this tongue-in-cheek look at what a web designers/developers time is spent doing on a project… Funny, but scarily realistic!

Stephen Fry on the Eee PC

2008-02-04T00:00:00+00:00

I really like the Eee PC – some people at work here have them, and if I could get it past the wife, i’d happily have one! ;)

Seems like the well spoken geek Stephen Fry is quite a fan too:

I am writing this article on a kind of mini John the Baptist, a system that prepares the way of the software saviour whose coming will deliver the 90% of world computer users who suffer under Windows from the expensive, clumsy, costly, ugly, pricey toils of Microsoft.

The Asus EEE PC perched on my knee combines GNU software with a Linux kernel powered by an Intel Celeron Mobile Processor to produce a very extraordinary little laptop. It weighs less than a kilogram, starts up from cold in about 12 seconds and shuts down in five. It has no internal hard disk and no CD drive. It offers 512MB of RAM, 4GB of storage and a seven-inch display; wireless, dial-out modem and ethernet adaptors are available for networking and internet connections, three USB ports, mini-jack sockets for headphones and microphone, a VGA out, an SD card slot and a built-in webcam. All for about £200 – less than the price of a show, dinner and taxi for two in London’s West End.

SitePoint CSS Reference

2008-01-29T00:00:00+00:00

Check out the SitePoint CSS Reference – useful for anyone writing CSS.

Hiding Keynote Presentations

2008-01-29T00:00:00+00:00

I don’t give many presentations these days, but this is a great tip:

If you give many presentations on the Mac, chances are you’re using Apple’s Keynote presentation software. One cool feature in Keynote is the ability to demo something on your Mac without giving away your next slide or notes. When you’re in the middle of a presentation, just hit the “h” key on your keyboard. This will hide the entire Keynote application and show your desktop.

When you press the h key, the Keynote icon in the dock will change and include a play button. When you want to resume your presentation, just click the Keynote icon in the dock.

Is the MacBook Air THAT Bad?!?

2008-01-25T00:00:00+00:00

Finally, a common sense response to all of these MacBook Air bashing articles. I admit – I don’t want one, i’d rather have a ‘regular’ MacBook or a MacBook Pro, but there are people out there that would want something like this…

Direct from the Canadian Ministry of Silly Punditry we learn that the MacBook Air may increase risk of laptop loss (tip o' the antlers to Colin Morton).

Indeed. The only way to ensure your laptop won’t get stolen is to buy big fat honkin' ugly ones.

But, clearly, neither of those beats this gem from PC World’s Mike Barton:

MacBook Air Amiss: Time to License Mac OS X?

Good question! Like “I Have Stubbed My Toe And Find It Painful: Time to Commit Suicide?”

SPARQL Graduates to W3C Recommendation

2008-01-17T00:00:00+00:00

I watched a presentation on this about 18 months ago at a conference and it looked pretty interesting – some good potential applications in the scientific field. Glad to see things are progressing.

“The W3C just gave SPARQL the stamp of approval. SPARQL is a query language for the Semantic Web, and differs from other query languages in that is usable across different data sources. There are already 14 implementations of the spec available. Most of them are free software. There are also billions of relations out there that are query-able, thanks to the Linking Open Data project. The structured data of Wikipedia is now query-able at DBpedia. Also, have a look at Ivan Herman’s presentations on this topic.”

CSS Gradient Text Effect

2008-01-17T00:00:00+00:00

Found this in my feeds today – genius way of making very stylish headings without resorting to image replacement.

Do you want to create fancy headings without rendering each heading with Photoshop? Here is a simple CSS trick to show you how to create gradient text effect with a PNG image (pure CSS, no Javascript or Flash). All you need is an empty <span> tag in the heading and apply the background image overlay using the CSS position:absolute property. This trick has been tested on most browsers: Firefox, Safari, Opera, and even Internet Explorer 6. Continue to read this article to find out how.

Britain Advises Against Vista, Office 2007 for Schools

2008-01-12T00:00:00+00:00

Although I do have to admit to liking MS Office (and indeed MS Office 2007 is good), I have to agree with this recommendation. There is pretty much nothing MS Office could do that OpenOffice could not do for you in a school setting – so why shell out all that money for Office licenses and force the kids parents to as well (or resort to dodgy copies) when free software is good enough. And as for Vista… Linux has my vote for schools every time.

Britain Advises Against Vista, Office 2007 for Schools: “An anonymous reader writes ‘The British government’s educational IT authority has issued a report advising schools in the country not to upgrade their classroom or office systems to Windows Vista or Office 2007. According to this InformationWeek story, the British Educational Communications and Technology Agency says costs for Vista and Office 2007 'are significant and the benefits remain unclear.’ Instead, Becta is advising British schools to take a long look at Linux and open source suites like OpenOffice.org.”

SSH Shared-Key Setup - SSH Logins Without Passwords

2008-01-10T00:00:00+00:00

SSH is a great tool for remotely accessing another machine, but entering your password every time you log into a remote box can be a pain if you would like to set-up some background scripts to connect to a server and do something (i.e. a backup script running as a cron job). Here’s how I set-up my Mac to be able to log into my server without the need for a password to be entered each time – the instructions should be good for any variant of Unix/Linux, but you need to take into account path names etc. on your machine.

The first thing we will do is generate a key for the SHH version 1 protocol (just in case you are connecting to an older machine):

ssh-keygen -t rsa1

SSH-Keygen will respond with something like the following:

Generating public/private rsa1 key pair.
Enter file in which to save the key (/Users/daz/.ssh/identity):

At this point hit enter then you will be prompted for a passphrase – this is a form of password that will be used to generate your unique keys and can contain any set of characters and spaces – something like "I’m really liking all of this geeky nonsense!" is a perfectly acceptable passphrase – just whatever you do, don’t use an empty passphrase. After entering (and confirming) your passphrase you will get the following output:

Your identification has been saved in /Users/daz/.ssh/identity.
Your public key has been saved in /Users/daz/.ssh/identity.pub.

This means that our identity keys have been generated. Now we just need to create a pair of keys for the SSH2 protocol – you can use the same or different passphrases for these keys – it’s up to you…

ssh-keygen -t dsa

Then

ssh-keygen -t rsa

You should now have three sets of keys in your ~/.ssh directory, the ones with the .pub extension are your public keys (what we need to put on your other machines) and the others are your private keys – these must be kept safe!

So, let’s use scp to copy the files across:

scp ~/.ssh/*.pub daz@MyServer:/home/daz/

Then log into your server using ssh and issue the following commands:

cat identity.pub >>~/.ssh/authorized_keys
cat id_dsa.pub >>~/.ssh/authorized_keys
cat id_rsa.pub >>~/.ssh/authorized_keys
rm identity.pub id_dsa.pub id_rsa.pub

This populates the authorized_keys file on our server with the three public keys that we have just transferred and then removes them as they’re no longer needed here.

That’s everything done, now all we have to do is log out of our server, and then try and log back in via ssh – a password should no longer be required!^* :)

^* This isn’t strictly true – on OS X it asks you for the id_rsa passphrase that we established before, you will need to enter this, but you can then have it stored in the keychain for hassle free use from here.

NetNewsWire's Now Freeware

2008-01-10T00:00:00+00:00

This is great news – NetNewsWire, the best news reader on the Mac is now completely free! Not just the ‘Lite’ version anymore, but the full product! This is my default (and only) news reader on the Mac.

There’s a FAQ that explains a bunch of things I’m not going to repeat it all here.

But I will say that, for me personally, this is a dream come true. Every developer wants to be able to work on the software they love, make a living at it, and give it to the world for free.

Usually you get to pick two out of three if you’re lucky. Me, I get all three.

A better ls for Mac OS X

2008-01-04T00:00:00+00:00

I’m a bit of a command-line freak and like to spend a fair amount of time with the terminal open… As such I like to spend a small amount of time getting the terminal set-up nicely. Other than changing the default colour scheme and font, one (slightly) more drastic change is to replace the standard implementation of ls for one that is slightly more configurable.

The default ls on OS X comes from BSD and compared to the GNU/Linux alternative is slightly lacking when it comes to changing how things look – so what I like to do is replace it with the GNU ls available in MacPorts – this allows me to get a terminal setup like below:

To get this done is pretty simple, once you have MacPorts set up correctly (if you can type man port and get a manual page you’re ready), just run the following command:

sudo port install coreutils +with_default_names

This installs the ‘GNU File, Shell, and Text utilities’ which ls is part of – the extra option at the end +with_default_names makes it override (only override – not replace, this is totally removable) the default ls and other tools otherwise they will have a ‘g’ prefix – i.e. ls would be gls.

Next we add some extra configuration to our ~/.bash_profile file (i’ll include my MacPorts config in case you get stuck above)…

# MacPorts
export PATH=/opt/local/bin:/opt/local/sbin:$PATH
export MANPATH=/opt/local/share/man:$MANPATH

# Terminal colours (after installing GNU coreutils)
NM="\[\033[0;38m\]" #means no background and white lines
HI="\[\033[0;37m\]" #change this for letter colors
HII="\[\033[0;31m\]" #change this for letter colors
SI="\[\033[0;33m\]" #this is for the current directory
IN="\[\033[0m\]"

export PS1="$NM[ $HI\u $HII\h $SI\w$NM ] $IN"

if [ "$TERM" != "dumb" ]; then
    export LS_OPTIONS='--color=auto'
    eval `dircolors ~/.dir_colors`
fi

# Useful aliases
alias ls='ls $LS_OPTIONS -hF'
alias ll='ls $LS_OPTIONS -lhF'
alias l='ls $LS_OPTIONS -lAhF'
alias cd..="cd .."
alias c="clear"
alias e="exit"
alias ssh="ssh -X"
alias ..="cd .."

Then finally we need to create a file called .dir_colors in our home directory that allows us to configure the colours used by ls:

touch ~/.dir_colors

Then add the contents of the file here:

# Configuration file for dircolors, a utility to help you set the
# LS_COLORS environment variable used by GNU ls with the --color option.

# The keywords COLOR, OPTIONS, and EIGHTBIT (honored by the
# slackware version of dircolors) are recognized but ignored.

# Below, there should be one TERM entry for each termtype that is colorizable
TERM linux
TERM linux-c
TERM mach-color
TERM console
TERM con132x25
TERM con132x30
TERM con132x43
TERM con132x60
TERM con80x25
TERM con80x28
TERM con80x30
TERM con80x43
TERM con80x50
TERM con80x60
TERM xterm
TERM xterm-color
TERM xterm-debian
TERM rxvt
TERM screen
TERM screen-w
TERM vt100

# Below are the color init strings for the basic file types. A color init
# string consists of one or more of the following numeric codes:
# Attribute codes:
# 00=none 01=bold 04=underscore 05=blink 07=reverse 08=concealed
# Text color codes:
# 30=black 31=red 32=green 33=yellow 34=blue 35=magenta 36=cyan 37=white
# Background color codes:
# 40=black 41=red 42=green 43=yellow 44=blue 45=magenta 46=cyan 47=white
NORMAL 00   # global default, although everything should be something.
FILE 00     # normal file
DIR 01;36   # directory
LINK 01;37  # symbolic link.  (If you set this to 'target' instead of a
            # numerical value, the color is as for the file pointed to.)
FIFO 40;33  # pipe
SOCK 01;35  # socket
DOOR 01;35  # door
BLK 40;33;01    # block device driver
CHR 40;33;01    # character device driver
ORPHAN 40;31;01 # symlink to nonexistent file

# This is for files with execute permission:
EXEC 01;35

# List any file extensions like '.gz' or '.tar' that you would like ls
# to colorize below. Put the extension, a space, and the color init string.
# (and any comments you want to add after a '#')

# If you use DOS-style suffixes, you may want to uncomment the following:
#.cmd 01;32 # executables (bright green)
#.exe 01;32
#.com 01;32
#.btm 01;32
#.bat 01;32

.tar 01;31 # archives or compressed (bright red)
.tgz 01;31
.arj 01;31
.taz 01;31
.lzh 01;31
.zip 01;31
.z   01;31
.Z   01;31
.gz  01;31
.bz2 01;31
.deb 01;31
.rpm 01;31
.jar 01;31
.dmg 01;31

# image formats
.jpg 01;35
.png 01;35
.gif 01;35
.bmp 01;35
.ppm 01;35
.tga 01;35
.xbm 01;35
.xpm 01;35
.tif 01;35
.png 01;35
.mpg 01;35
.avi 01;35
.fli 01;35
.gl 01;35
.dl 01;35

# source code files
.pl 00;33
.PL 00;33
.pm 00;33
.tt 00;33
.yml 00;33
.sql 00;33
.html 00;33
.css 00;33
.js 00;33

Finally, all you need to do is close and re-open the Terminal. Now we should be sorted. :)

Active Scaffold Ajax CRUD Interfaces for Ruby on Rails

2007-12-30T00:00:00+00:00

This could be most useful in the near future…

Most web applications have many more model objects exposed on the backend, or admin side, than they do on the front. Coding interfaces for all those models is redundant and a waste of resources when all you need is CRUD functionality that’s smart enough to handle all your ActiveRecord associations.

ActiveScaffold is a Ruby on Rails plugin that provides you with a wealth of dynamically created goodness, just plug the ActiveScaffold into your controller, you can have a AJAXified table interface for creating, updating, and deleting objects then. It has the following main features as well.

Automatic handling of ActiveRecord associations

Sorting, Search and Pagination

Graceful JavaScript degradation

RESTful API support (XML/YAML/JSON) baked in

Sexy CSS styling and theming support

Getting your DVDs onto your Mac/iPod/iPhone

2007-12-29T00:00:00+00:00

I’d looked at Handbrake a while back but the GUI was far too confusing for a simpleton like me. It seems like it’s been cleaned up quite a bit now and looks rather useful! (The little video giving an overview of how to work things helps too!)

Handbrake is one of those applications that we adore here at TUAW HQ. It makes converting DVDs into a variety of digital files a snap (though only use it with DVDs you own. Don’t be pirates, kids). Chris Breen, of Macworld fame (and an amateur astronomer it would seem) shows us how to use HandBrake like a pro. Breen goes a step beyond ‘use the presets’ and delves into what many of the options HandBrake offers up actually do, and how they impact your files.

Google Chart API

2007-12-13T00:00:00+00:00

The chaps over at Google have come up with a neat webservice – an easy way to get charts onto your webpages, the Google Chart API.

Google has finally released Google Charts API, which returns a PNG-format image in response to a URL. Several types of image can be generated: line, bar, and pie charts for example. For each image type you can specify attributes such as size, colors, and labels.

You can include a Chart API image in a webpage by embedding a URL within an <img> tag. When the webpage is displayed in a browser the Chart API renders the image within the page.

Flot: Pure Javascript Plotting Library

2007-12-13T00:00:00+00:00

Yet more chart drawing goodness. This takes a different approach to the Google model by generating really good looking graphs all on the client-side in javascript – very nice!

Flot is a pure Javascript plotting library for jQuery. It produces graphical plots of arbitrary datasets on-the-fly client-side. The focus is on simple usage (all settings are optional), attractive looks and interactive features like zooming. Although Flot is easy to use, it is also advanced enough to be suitable for Web 2.0 data mining/business intelligence purposes which is its original application. The plugin is targeting all newer browsers.

Microformats Plugin for Safari

2007-11-29T00:00:00+00:00

I’m a fan of the Tails plugin for Firefox… Now Safari (on Leopard) gets its own Microformats Plugin! :)

Of course, in order to take advantage of Microformats and perhaps bring the information they offer onto your system, you need a browser that will read them – there’s Firefox plugins, and NetNewsWire 3.0’s built-in browser reads them. But what about Safari? Thanks to SIMBL, there’s a small array of Safari plugins available and from the maker of Safari Tidy comes Safari Microformats. Whenever visiting a site with Microformats, an icon appears in the right of the address bar (not unlike the RSS icon). Clicking it brings up a menu of available hCards and hCalendars you can add to Address Book and iCal.

Google Maps for Mobile Adds Positioning

2007-11-29T00:00:00+00:00

Sounds like a good new feature…

Google is set on Wednesday to launch a new feature in its Google Maps for Mobile program that automatically sets your location even in phones that lack a global positioning system (GPS) device.

Until now, if you were in a cafe and you wanted to search for a nearby photocopy shop, you had to type in an address to set your location before Google Maps for Mobile could provide local listings.

The beta feature triangulates your approximate location based on nearby cell towers so you don’t have to type in your address. Given that less than 15 percent of mobile phones are GPS-enabled, this feature will be helpful to many people.

Darwin Calendar Server

2007-11-29T00:00:00+00:00

At the moment I’m a very happy user of Google calendar and Spanning Sync for all my scheduling needs. But the geek in me fancies playing about with things so I’m thinking about setting up a CalDav server (when time permits) so Cat and I can organise our lives accordingly.

Here’s some pages I’ve been reading whilst doing my research.

Will possibly post more as and when I get a chance to play about with things…

Color Wizard - Colour Scheme Generator

2007-11-29T00:00:00+00:00

Color Wizard is an online colour scheme generator.

There are many of these kind of tools around, but I quite like interface on this one. The randomise feature is also quite useful.

Quick Look Folder and Zip plugins

2007-11-27T00:00:00+00:00

This is yet another example of why I want to upgrade to Leopard…

Quick Look is a beautiful thing, and in my view practically itself worth the cost of admission to Leopard. Unfortunately, the more you get used to it, the more annoying it is when you get to a file format that Quick Look doesn’t support. Fortunately, Apple was smart enough to design Quick Look with an open architecture that allows developers to write their own plugins and support more file formats, which Japanese developer Taiyo used to write two excellent plugins.

The first addresses a serious annoyance with the default Quick Look implementation on folders. If you invoke Quick Look with a folder selected in the Finder you’ll get…a picture of the folder icon. Frankly, that’s pretty stupid. Taiyo’s Folder Quick Look Plugin fixes this by displaying the folder’s contents, which is how it should have been done in the first place. Likewise, Taiyo’s Zip Quick Look Plugin displays the contents of zip files.

IconGrabber

2007-11-27T00:00:00+00:00

IconGrabber is a useful little application for getting an OS X applications icon for use on the web. It’s also available as a Quicksilver plugin.

It couldn’t be easier. Just drop the file or folder that you want the icon from onto IconGrabber, and choose a place to save it. The extension you choose determines the format, otherwise it defaults to tiff. That’s it!

Ack, a Grep Replacement

2007-11-27T00:00:00+00:00

Ack is a grep alternative, written in pure Perl, using Perl’s regular expressions to do your searches (just one of the long list of reasons to use this over grep). I think i’ll be using this then…

ack is a tool like grep, aimed at programmers with large trees of heterogeneous source code. ack is written purely in Perl, and takes advantage of the power of Perl’s regular expressions.

Getting Gmail IMAP Running Nicely

2007-11-19T00:00:00+00:00

I’ve just managed to get my Gmail service upgraded to the new version with IMAP support, (If you’re a user in the UK like me and are still waiting for your Gmail service to upgrade, simply navigate into your Gmail settings and change your language settings from ‘English (UK)’ to ‘English (US)’. This should make your Gmail switch to version 2 instantly!) and as such i’ve been trawling the net for information on how to get this all set-up nicely. By this I mean moving my mail filtering rules onto Gmail itself and getting IMAP to play a bit more nicely with Apple Mail…

Here’s how to get Apple Mail to work as expected, thanks to 5ThirtyOne:

Similar steps must be taken to ensure that any emails sent, saved as drafts, or deleted are properly identified by Gmail’s servers. After completing the IMAP setup steps for Apple Mail, instructing Mail is a few simple clicks away. Once your Gmail IMAP account is added to Mail, you’ll notice your [Gmail account] in the left sidebar.

Highlight ‘[Gmail] Sent Mail’ in the sidebar and select ‘Mailbox’ (menu bar) > ‘Use This Mailbox For’ > ‘Sent’.

Highlight ‘[Gmail] Drafts’ in the sidebar and select ‘Mailbox’ (menu bar) > ‘Use This Mailbox For’ > ‘Drafts’

Highlight ‘[Gmail] Trash’ in the sidebar and select ‘Mailbox’ (menu bar) > ‘Use This Mailbox For’ > ‘Trash’

Highlight ‘[Gmail] Spam’ in the sidebar and select ‘Mailbox’ (menu bar) > ‘Use This Mailbox For’ > ‘Junk’

Once properly configured, managing email from Apple Mail or the iPhone will be no different from managing emails within the Gmail web client – sent, drafts, trash, and junk properly sorted between your various email clients and web interface.

Read the full article for even more information (including iPhone set-up).

And the best hints for setting up slightly more complex filters in Gmail came from Lifehacker:

I needed to set up a filter that would apply label ‘work’ to any email that came from ‘xyz@workplace.com’ OR had the word ‘workoholic’ in it. Unfortunately, Gmail’s inbuilt ‘Create a filter’ feature’s dialog boxes are connected with an AND operator. Example: if I wrote ‘ xyz@workplace.com’ in the ‘from:’ field of the ‘Create a filter’ page, and ‘workoholic’ in the ‘Has the words:’ field, then only emails that came from ‘xyz@workplace’ AND had the word ‘workoholic’ would be picked up by this filter. So, to get the desired result, I needed TWO filters. Unless…

[…]

Incorporate both the conditions in the ‘Has the words:’ field itself! So my ‘Has the words’ field reads as: (from:(xyz@workplace.com) OR (workoholic)). Voila! c'est fini! But the possibilities are endless!

Read the full article for more information.

Top 10 Quicksilver Plugins

2007-11-18T00:00:00+00:00

I love Quicksilver, it’s one of those applications that makes working on the Mac really really great. Lifehacker has a quick rundown on 10 of the best plugins to help improve your Quicksilver experience:

Open source Mac utility Quicksilver isn’t just an application launcherâ€”it’s a comprehensive keyboard interface. Launching applications and documents is just Quicksilver’s gateway drug: The more you get used to doing things with Quicksilver, the more things you want to do with it. Out of the box Quicksilver comes with the barest essentials, but once you add the right plug-ins that interact with menus, apps, documents, and settings, you can accomplish more and more complex tasks from that familiar three-paned prompt. After the jump, check out top 10 favorite Quicksilver plug-ins, and how to set them up.

CSS Styled Tables

2007-11-18T00:00:00+00:00

Veerle comes up with another look at styling tables with CSS. A great read.

In 2005 I wrote an article about styling a table with CSS. After receiving so many requests I finally decided to give in and write another tutorial. Seems like a popular topic and an interesting one to share some tricks on how you can nicely style them. This article is about the proper usage of tables, for tabular data. How you can implement them with accessibility in mind and how to make them appealing for the eye using CSS.

Mount ISO Files With Nautilus

2007-11-14T00:00:00+00:00

Here’s two short bash scripts that allow you to mount and unmount an ISO image easily within the right-click menu in Nautilus (the file manager in Gnome):

sudo mkdir /media/ISO
cd ~/.gnome2/nautilus-scripts/
gedit "Mount ISO Image"

Now paste this code into the file:

#!/bin/bash
#
for I in `echo $*`
do
foo=`gksudo -u root -k -m "enter your password for root terminal access" /bin/echo "got r00t?"`
sudo mount -o loop -t iso9660 $I /media/ISO
done
done
exit0

Save, and exit gedit.

gedit "Unmount ISO Image"

Then paste this code in this file:

#!/bin/bash
#
for I in `echo $*`
do
foo=`gksudo -u root -k -m "enter your password for root terminal access" /bin/echo "got r00t?"`
sudo umount $I
done
done
exit0

Save, and exit gedit. Now finally…

chmod a+x *

Now you can mount and unmount ISO files by using the ‘Scripts’ options in the right-click menu. :)

Thanks to the Ubuntu Blog for the information.

Install phpPgAdmin on Ubuntu 7.10

2007-11-14T00:00:00+00:00

Update: These instructions have been tested and work fine in the latest version of Ubuntu (8.04, Hardy Heron).

phpPgAdmin is a web based GUI for administrating a PostgreSQL database server.

Here’s some quick notes on getting it installed easily on Ubuntu 7.10…

In the terminal enter the following:

sudo apt-get install phppgadmin

This will set up and install all of the phpPgAdmin packages. It will also set-up and configure Apache and php5 for you too if you haven’t installed these already.

Next we need to create a symlink to phpPgAdmin so that Apache can find it:

sudo ln -s /etc/phppgadmin/apache.conf /etc/apache2/conf.d/phppgadmin.conf

Now if you navigate to http://localhost/phppgadmin you should be greeted with the phpPgAdmin screen. If your user account has a PostgreSQL account however, you will be logged in automagically.

Optionally, if you would like to be able to use the phpPgAdmin interface as the default ‘postgres’ administration account, (I am assuming here that you have set-up your PostgreSQL server using my set-up instructions and therefore have a password protected ‘postgres’ account and that logins require passwords.) you will need to do the following (Please make sure you understand the security implications of allowing this type of access to your database server – if you have not secured your administration accounts, do it now!)…

sudo gedit /usr/share/phppgadmin/conf/config.inc.php

Now find and change the following line

$conf['extra_login_security'] = true;

$conf['extra_login_security'] = false;

Save and close gedit. Now all you need to do is restart Apache.

sudo /etc/init.d/apache2 reload

Now if you head on over to http://localhost/phppgadmin all should be ready for you.

Zotero

2007-11-13T00:00:00+00:00

Zotero is a new reference management tool that comes in the form of a Firefox (and Flock) extension. It looks like it could be a very good (and free) alternative to commercial reference management software tools like Endnote and Reference Manager. It even has plugins for Word and OpenOffice for cite-while-you-write functionality, and Wordpress so that writers of Wordpress based blogs can ensure that their posts are cleanly imported for users of Zotero.

Zotero [zoh-TAIR-oh] is a free, easy-to-use Firefox extension to help you collect, manage, and cite your research sources. It lives right where you do your work – in the web browser itself.

If you have any potential use for reference management (i.e. if you are a student or scientist) – I seriously recommend checking this out.

Installing Apache and PHP Troubles

2007-11-13T00:00:00+00:00

I just recently set Apache up on my home server (more on the server at some point in the future), but I was having problems serving up php pages. Every time I tried to access a php based page, Firefox came up asking if I wanted to download a ‘.PHTML’ file!!! :(

Thankfully the answer (like most things with Ubuntu) was found on the Ubuntu Forums…

Simply edit the file /etc/apache2/apache2.conf by adding the following line:

AddType application/x-httpd-php .php .phtml

Now php files should be handled by the server in the way that they were intended.

American Style Pancakes

2007-11-12T00:00:00+00:00

These are a great idea for a quick and easy dessert when there’s nothing else to hand (they saved me last night)! Cheers to Celia for the recipe.

Ingredients

2 ½ cups flour
¼ cup sugar
1 Tbsp baking powder
½ tsp salt
2 cups milk or buttermilk
2 eggs – beaten
1/3 cup vegetable oil

Method

Mix dry ingredients in a large bowl.
Mix all liquid ingredients in another bowl.
Add wet to dry ingredients and stir until mixed. (If the batter looks too thick add water or milk a little at a time until you get the consistency that you want). Let rest for about 10-15 minutes.
Pour onto medium hot greased pan. Once bubbles cover the surface, flip the pancake, cover pan and lower heat for about 1 minute. The cover will help the pancake to rise more.
Remove from pan and serve with butter and syrup.

A First Look at Android

2007-11-12T00:00:00+00:00

I really thought that Android was going to be a complete turkey, but after watching some of the videos up on YouTube it does look like it could be quite promising. If someone releases some decent hardware at a reasonable price the iPhone could have some competition…

Stacks Overlays

2007-11-11T00:00:00+00:00

This is a great idea to improve the appearance (and usability) of stacks in Leopard.

Stacks is pretty much Leopard’s only non-eyecandy change to the dock, and it had the potential to be pretty handy, but the fact that the icon representing the stack is whatever the top file in the folder happens to be really ruins it (for me at least). However, if you haven’t yet given up on stacks and thrown them off your dock, there is a solution: overlaying stacks icons.

In essence, these are just small-ish semi-transparent icons that are permanently our top icon. This picture explain it best (before & after):

Stephen Fry on the iPhone

2007-11-10T00:00:00+00:00

Stephen Fry:

I have been using an Apple iPhone now for more than four months. This is due to an unhealthy mixture of friendship with its designer, a slobbery and pathetic love of the new, the possession of an American billing address (necessary until today for the activation and use of the device) and a willingness to pay preposterous international roaming charges. It puts me in a good position however, to tell you what you’re in for if you decide to own one of these honeys.

Broken Arrow

2007-11-08T00:00:00+00:00

Note to self: Buy Broken Arrow on DVD. Caught a bit of it on TV last night – I forgot just how damn good that film is! (The soundtrack is great too)!

Use Folder Icons in Leopard Stacks

2007-11-06T00:00:00+00:00

Peter N Lewis:

The Leopard Dock shows folders as a layer of icons, which is crazy for folders as you cannot easily recognize a folder based on its contents. Especially crazy when the folders have recognizable icons already!

Of course, here at Stairways we prefer to find solutions to problems rather than just grumble, so here is a trivial solution. Simply create an alias to the folder, name it to sort as the first icon, and put it in the folder.

Update: Here’s another way to achieve the same idea, but with icons sorted by date – i.e. the downloads stack.

Massive Data Loss Bug in Leopard

2007-11-06T00:00:00+00:00

I’ve been reading about this in a few places now.

Leopard’s Finder has a glaring bug in its directory-moving code, leading to horrendous data loss if a destination volume disappears while a move operation is in action. I first came across it when Samba crashed while I was moving a directory from my desktop over to a Samba mount on my FreeBSD server.

This is why you should NEVER just move data from one drive to another – copy it first, only then delete the original.

Use Leopards Quick Look from the Terminal

2007-11-05T00:00:00+00:00

Useful info from over at the Unofficial Apple Weblog:

TUAW reader Shaun Haber sent us a link to his personal blog with a great post about using Leopard’s Quick Look from the command line, which is wonderfully handy for anyone who spends a chunk of their day in Terminal. The qlmanage utility gives you direct access to many Quick Look functions; of specific interest is the -p flag. This option displays the Quick Look generated preview for any file. So if you tell it to qlmanage -p foo.png, the image immediately pops up in a Quick Look pane.

Even better, Quick Look supports slide shows. So if you cd into a folder of images and run qlmanage -p *.jpg, you’ll be rewarded with a full-on presentation of your pictures.

Other qlmanage flags of interest include -h (displays a help message) -t (thumbnail generation) and -f (a zoom factor to display with).

The downside of qlmanage is that it’s full of NSLog-style messages. Haber recommends you pipe the output into /dev/null as follows: qlmanage -p *.jpg >& /dev/null.

Phantom Hourglass Review

2007-11-05T00:00:00+00:00

I’ve been looking forward to the release of the latest in the Zelda series.

Of all the titles in the Legend of Zelda series, some of the most-respected have been for handheld consoles. Link’s Awakening, the Oracle duo, and Minish Cap all manage to combine on-the-road gaming with a certain purity of Zelda-ness. Link’s most recent adventure on the small screen, Phantom Hourglass, generally continues this tradition and introduces a number of new elements to the property. Unique controls, a true sequel, and cel-shaded graphics all make Hourglass stand out from ‘traditional’ Zelda games, and together the whole hangs together fairly well.

Is a Domain Name an Automatic Trademark?

2007-11-05T00:00:00+00:00

Just read this post on Slashdot:

“I registered a descriptive domain name (something like "thesimpledog.com”) and started a blog on it. About a month later I get a threatening letter from a link farmer who owns “simpledog.com” The owner of simpledog.com is claiming that he owns the trademark to the words simpledog even though he has no real business or rights by that name other than a static page with some text and Adsense slapped on it. There is no product, service or brand whatsoever. Does simply registering a two or three word domain give you instant trademark rights to those words even though you’ve never done anything with them? Should I give up my domain to a link farmer who is trying to bully me, or does he have a valid right to any phrase he registers that isn’t already trademarked?"

My opinion – tell him where to go. I thought the idea of a trademark was that you had to actively be using that name in a trade? He has no brand, no real business using that name (you can’t claim a static page full of AdSense links is a real business), and no product. He doesn’t have any sort of case, he’s just trying to bully the guy into give over his domain name… I hate stuff like this, when I was looking for a new domain name, every decent name I thought of was home to some troll like this. :(

Install PostgreSQL on Ubuntu 7.10

2007-11-05T00:00:00+00:00

If you are using the latest version of Ubuntu (8.04 - Hardy Heron), you might find these slightly updated instructions useful.

Before we move on, this guide was tested on the current release of Ubuntu Linux, (7.10 – Gutsy Gibbon) and PostgreSQL 8.2, but it should also be applicable to older versions (of Ubuntu and PostgreSQL) and other Debian based distros.

Right for the basic installation, at the command-line, enter the following commands (or search for the listed packages in synaptic if you prefer that way of working):

sudo apt-get install postgresql postgresql-client postgresql-contrib
sudo apt-get install pgadmin3

This installs the database server/client, some extra utility scripts and the pgAdmin GUI application for working with the database.

sudo su postgres -c psql template1
template1=# ALTER USER postgres WITH PASSWORD 'password';
template1=# \q

That alters the password for within the database, now we need to do the same for the unix user ‘postgres’:

sudo passwd -d postgres
sudo su postgres -c passwd

Now enter the same password that you used previously.

sudo su postgres -c psql < /usr/share/postgresql/8.2/contrib/adminpack.sql

sudo gedit /etc/postgresql/8.2/main/postgresql.conf

Now, to edit a couple of lines in the ‘Connections and Authentication’ section…

Change the line:

#listen_addresses = 'localhost'

listen_addresses = '*'

and also change the line:

#password_encryption = on

password_encryption = on

Then save the file and close gedit.

sudo gedit /etc/postgresql/8.2/main/pg_hba.conf

Comment out, or delete the current contents of the file, then add this text to the bottom of the file:

# DO NOT DISABLE!
# If you change this first entry you will need to make sure that the
# database
# super user can access the database using some other method.
# Noninteractive
# access to all databases is required during automatic maintenance
# (autovacuum, daily cronjob, replication, and similar tasks).
#
# Database administrative login by UNIX sockets
local   all         postgres                          ident sameuser
# TYPE  DATABASE    USER        CIDR-ADDRESS          METHOD

# "local" is for Unix domain socket connections only
local   all         all                               md5
# IPv4 local connections:
host    all         all         127.0.0.1/32          md5
# IPv6 local connections:
host    all         all         ::1/128               md5

# Connections for all PCs on the subnet
#
# TYPE DATABASE USER IP-ADDRESS IP-MASK METHOD
host    all         all         [ip address]          [subnet mask]  md5

That’s it, now all you have to do is restart the server:

sudo /etc/init.d/postgresql-8.2 restart

And all should be working.

Creating New Accounts in PostgreSQL

2007-11-05T00:00:00+00:00

Getting a new account set up on PostgreSQL is a simple process…

Create our new user:

sudo su postgres -c createuser daz

Then you have to give this new user role a name (I called it daz), and then say ‘y’ to the question “Shall the new role be a superuser?” if you want the user to be an administrator.

Give the user a database password (this does not have to be the same as their unix password):

sudo su postgres -c psql
postgres=# ALTER USER daz WITH PASSWORD 'mypassword';
postgres=# \q

Finally, give the new user a database to play with:

sudo su postgres -c createdb daz

Pretty straight forward… :)

EVE Online for Mac/Linux on Tuesday

2007-11-04T00:00:00+00:00

Ohhhh, I always fancied looking at EVE. Now all I need to do is get the PhD thesis out of the way and I might have enough time to look into it. :)

The official EVE Online site has details of upcoming patch ‘Revelations 2.3’. Along with a number of bug-fixes to the PvP-focused Massively Multiplayer Online Game, this game fix will offer up compatibility with Mac OS X and Linux. Though the Mac client is a native port, Linux will require the used of Cedega. The post suggests that if you’d like a preview of what the game will be like on your rig, you can download the client and tool around the test server. System requirements are also listed, as are the distributions of Linux they are specifically supporting: Ubuntu 7+, Suse 10+, and Linspire 6.

iPhone "Invention of the Year"???

2007-11-03T00:00:00+00:00

I like the look of the iPhone – I want one even. But it’s hardly the single greatest invention of the year… Thankfully someone out there has put some reasonable thought into this:

Invention of the year. Take some time and dwell on that statement for a moment. Not invention of the month. Not invention of the week. Not gadget of the year. Invention of the year!

…

The iPhone may be “pretty” but it certainly does not reduce pollution, protect people from hurricanes, distributes solar energy, or allow an amputee to have a finger.

This is not to say the iPhone isn’t amazing but to give it Time Magazine’s Invention of the Year is truly an embarrassment to the magazine.

Definately gadget of the year – but no way invention of the year. There are much more worthy examples in the article, let’s face it, the iPhone won because it’ll sell magazines. I sometimes wonder about the culture of today…

Installing VMware Tools on Ubuntu Gutsy

2007-11-03T00:00:00+00:00

I’ve just started to play about with the new Ubuntu (7.10 – Gutsy), I have to say that I quite like it – I was a big fan of Feisty and all other Ubuntu releases previously, so this is more of the same good stuff.

As I’m working with VMWare Fusion, the first thing that needs to be done is install the VMWare Tools. This is quite simply done with the following lines in the terminal once you have started your VM and mounted the tools image (Virtual Machine > Install VMWare Tools in the menu):

sudo aptitude update
sudo aptitude install build-essential linux-headers-$(uname -r)
cp -a /media/cdrom/VMwareTools* /tmp/
cd /tmp/
tar -vxzf VMwareTools*.gz
cd vmware-tools-distrib/
sudo ./vmware-install.pl

The just accept all of the defaults for the installation package.

Cheers to Ubuntu Tutorials for the info.

And the Fastest Vista Laptop is...

2007-11-03T00:00:00+00:00

I just love articles like this…

The fastest Windows Vista notebook we’ve tested this year is a Mac. Try that again: The fastest Windows Vista notebook we’ve tested this year – or for that matter, ever – is a Mac. Not a Dell, not a Toshiba, not even an Alienware. The $2419 (plus the price of a copy of Windows Vista, of course) MacBook Pro’s PC WorldBench 6 Beta 2 score of 88 beats Gateway’s E-265M by a single point, but the MacBook’s score is far more impressive simply because Apple couldn’t care less whether you run Windows.

Adding/Deleting Rows In TableKit Tables Revisited

2007-11-01T00:00:00+00:00

TableKit is a great javascript library for making your HTML tables fully editable. However, one problem is that you can’t add or delete rows from the tables…

I came up with a solution to this not so long ago, but it still had a problem – TableKit caches the tables on loading, so after we update the table body (adding or deleting a row) the sorting and editing of the table is completely screwed! :( However, with a little more work, and some help from one of the guys in the office – we’ve finally got this cracked! :)

The basic idea to the fix is, instead of updating the table body, replace the entire table with a new one and get TableKit to do its stuff on the new table. Although this is not the ideal solution (That would be knowing more about javascript and the dom so that we can make changes to TableKits cache as we update the table body – thus keeping the original table) – this does work quite well. Here’s the details (We’re using the code from the previous post as a starting point).

First, we’ll update the code from our template file (/root/src/users/list.tt):

[% META title = 'User List' -%]

<div id="users_div">
  <table id="users" class="sortable resizable editable">
    <thead>
      <tr>
        <th id="id" class="sortfirstasc noedit">Id</th>
        <th id="firstname">First Name</th>
        <th id="lastname">Last Name</th>
        <th class="noedit nocol"></th>
      </tr>
    </thead>
    <tfoot>
      <tr>
        <th>Id</th>
        <th>First Name</th>
        <th>Last Name</th>
        <th class="nocol"></th>
      </tr>
    </tfoot>
    <tbody id="user_body">
    [% FOREACH user IN users -%]
      <tr id='[% user.id %]'>
        <td>[% user.id %]</td>
        <td>[% user.firstname %]</td>
        <td>[% user.lastname %]</td>
        <td class="nocol">
          <a class="delete" href="#" onclick="deleteUser([% user.id %]); return false">delete</a>
        </td>
      </tr>
    [% END -%]
    </tbody>
  </table>
</div>
<br />
<a class="add" href="#" onclick="addUser(); return false">add a user</a>

Then add this javascript code to the bottom of the same file:

var users_table = new TableKit( 'users', {
  editAjaxURI: '[% c.uri_for('/users/_update_user') %]'
});

function addUser() {
  var timestamp = new Date().getTime();
  var new_table = 'users' + timestamp;
  var url = '[% c.uri_for('/users/_add_user') %]?timestamp=' + timestamp;
  new Ajax.Updater( 'users_div', url, {
    asynchronous: true,
    onComplete: function() {
    new TableKit( new_table, {
      editAjaxURI: '[% c.uri_for('/users/_update_user') %]'
    })
    }
  });
}

function deleteUser( user_id ) {
  var timestamp = new Date().getTime();
  var new_table = 'users' + timestamp;
  var url = '[% c.uri_for('/users/_delete_user/') %]?user_id=' + user_id + '&timestamp=' + timestamp;
  var answer = confirm('Are you sure you want to delete this user?');
  if (answer) {
    new Ajax.Updater( 'users_div', url, {
      asynchronous: true,
      onComplete: function() {
        new TableKit( new_table, {
          editAjaxURI: '[% c.uri_for('/users/_update_user') %]'
        })
      }
    });
  }
}

The main differences in the above from last time round are as follows:

The ‘users’ table is now inside a div with the id ‘users_div’
The link to add a user now calls a javascript function rather than an Ajax.Updater call directly.
The functions to add and delete users are essentially the same:
They create a timestamp to individually identify the new table we are going to create (this is the most important thing here to remember)!
They then use an Ajax.Updater call to talk to the Perl controller and generate the new table with a row added or removed.
Once the Ajax.Updater is complete, TableKit is then called again to make our new table editable and sortable.

That’s the template sorted, now let’s look at the controller (/lib/MyApp/Controller/Users.pm):

package MyApp::Controller::Users;

use strict;
use warnings;
use base 'Catalyst::Controller';

=head1 NAME

MyApp::Controller::Users - Catalyst Controller

=head1 DESCRIPTION

Catalyst Controller.

=head1 METHODS

=cut

=head2 index

=cut

sub index : Private {
  my ( $self, $c ) = @_;
  $c->response->redirect('/users/list');
}

=head2 list

Fetch all user objects and pass to users/list.tt in stash to be displayed

=cut

sub list : Local {
  my ( $self, $c ) = @_;
  $c->stash->{users}    = [ $c->model('MyAppDB::Users')->all ];
  $c->stash->{template} = 'users/list.tt';
}

=head2 _update_user

Ajax method to update the users table

=cut

sub _update_user : Local {
  my ( $self, $c ) = @_;

  $c->model('MyAppDB::Users')->find( { id => $c->req->params->{id} } )
    ->update( { $c->req->params->{field} => $c->req->params->{value} } );

  $c->res->body( $c->req->params->{value} );
}

=head2 _delete_user

Ajax method to delete users from the users table

=cut

sub _delete_user : Local {
  my ( $self, $c ) = @_;

  # Look-up our user entry
  my $user =
    $c->model('MyAppDB::Users')->find( { id => $c->req->params->{user_id} } )
    ->delete();

  my $output =
    __return_all_users( $self, $c, $c->req->params->{timestamp}, 'null' );

  $c->res->body($output);
}

=head2 _add_user

Ajax method to add users to the users table

=cut

sub _add_user : Local {
  my ( $self, $c ) = @_;

  # create a new user...
  my $new_user = $c->model('MyAppDB::Users')->create(
    {
      id        => $c->req->params->{user_id},
      firstname => '[First Name]',
      lastname  => '[Last Name]'
    }
  );

  my $output = __return_all_users( $self, $c, $c->req->params->{timestamp}, $new_user->id );

  $c->res->body($output);
}

=head2 __return_all_users

Private method for the Users ajax interaction.
Returns a html table.

=cut

sub __return_all_users : Private {
  my ( $self, $c, $timestamp, $new_user_id ) = @_;

  my @users = $c->model('MyAppDB::Users')->all();

  my $html =
      '<table id="users'
    . $timestamp
    . '" class="sortable resizable editable">
    <thead>
      <tr>
        <th id="id" class="sortfirstasc noedit">Id</th>
        <th id="firstname">First Name</th>
        <th id="lastname">Last Name</th>
        <th class="noedit nocol"></th>
      </tr>
    </thead>
    <tfoot>
      <tr>
        <th>Id</th>
        <th>First Name</th>
        <th>Last Name</th>
        <th class="nocol"></th>
      </tr>
    </tfoot>
    <tbody id="user_body">';

  if ( scalar(@users) > 0 ) {
    for ( my $i = 0 ; $i < scalar(@users) ; $i++ ) {
      my $class;

      if ( $new_user_id && $users[$i]->id == $new_user_id ) {
        $class = 'new';
      }
      else {
        if   ( $i % 2 == 0 ) { $class = 'rowodd'; }
        else                 { $class = 'roweven'; }
      }

      $html .=
          "<tr class=\""
        . $class
        . "\" id=\""
        . $users[$i]->id . "\">
          <td>" . $users[$i]->id . "</td>
          <td>" . $users[$i]->firstname . "</td>
          <td>" . $users[$i]->lastname . "</td>
          <td class=\"nocol\">
              <a class=\"delete\" href=\"#\" onclick=\" deleteUser("
        . $users[$i]->id . "); return false\">delete</a>
          </td>
        </tr>";
    }
  }
  else {
    $html .=
      '<tr><td colspan="4" class="nocol">All Users Deleted</td></tr>';
  }

  $html .= '</tbody></table>';

  return ($html);
}

=head1 AUTHOR

Darren Oakley

=head1 LICENSE

This library is free software, you can redistribute it and/or modify
it under the same terms as Perl itself.

=cut

1;

The only real changes in the controller are a general code clean-up, and a slight change to the ‘__return_all_users’ method – this now returns a whole table (identified by the unique timestamped id that we generated in the javascript functions). Nothing really needed changing in the back-end.

There you go! Now our TableKit based tables can be used to not only edit entries in the database, we can now add and remove them! :)

The files used in this example can be found below.

Attached Files:

MyApp.zip – v3

K2 Styles Are In...

2007-10-30T00:00:00+00:00

Here are my old styles for Wordpress blogs and K2. Take a look at Bix, Chameleon, Coffee, Penguin, Slick, Sparkle and Stripe. (Note: They might be in need of a bit of an update to work with the latest releases of K2 – i’ll leave that as an exercise for anyone wanting to use them ;) ).

Apple Wireless Keyboard LED at 40x Magnification

2007-10-25T00:00:00+01:00

You know… I HAD been wondering this!!!

Ever wonder how the power LED shows through the aluminum of Apple’s new wireless keyboard when it’s on, but blends into the metal when it’s off? Here’s how.

Visualizing your DBIC schema

2007-10-19T00:00:00+01:00

What a great idea – will give this a bash next week…

If you want a somewhat pretty picture of your DBIC schema (with relationships drawn, of course), install GraphViz, SQL::Translator, and DBICx::Deploy from the CPAN, and then run:

$ dbicdeploy -Ilib MyApp::Schema ~/graphs GraphViz

~/graphs will then contain a .sql file that is actually a png of your schema. Rename it and see your schema in your favorite png viewing application.

Remove Case-Sensitivity In Oracle

2007-10-18T00:00:00+01:00

Oracle is a great RDBMS, but the fact that searches against the database are case-sensitive can be a pain in the butt. Here’s how you can make searches case-insensitive…

In SQL…

alter session set NLS_SORT=BINARY_CI;
alter session set NLS_COMP=LINGUISTIC;

For use in Perl::DBI…

use strict;
use DBI;

my $dbh = DBI->connect(
  'dbi:Oracle:schema_name',
  'user',
  'password',
  {
    RaiseError    => 1,
    AutoCommit    => 0,
    on_connect_do => [
      'alter session set NLS_SORT=BINARY_CI',
      'alter session set NLS_COMP=LINGUISTIC'
    ]
  }
) || die "Database connection not made: $DBI::errstr";

$dbh->disconnect();

It's Official - iPhone SDK Coming Soon

2007-10-18T00:00:00+01:00

Great news! Straight from the horses mouth, (well, Steve’s anyway) Apple have announced that an iPhone SDK will be coming in February.

Let me just say it: We want native third party applications on the iPhone, and we plan to have an SDK in developers' hands in February. We are excited about creating a vibrant third party developer community around the iPhone and enabling hundreds of new applications for our users. With our revolutionary multi-touch interface, powerful hardware and advanced software architecture, we believe we have created the best mobile platform ever for developers.

Update: if that dissapears (as there seems to be no permalink for this article), have a read of Mac Rumors copy of the whole article.

Spooks

2007-10-17T00:00:00+01:00

One of the only shows on TV worth watching these days came back onto the BBC last night, bloody hell was it good!

If you’ve never seen or even heard of spooks before, get yourself over to the wikipedia entry, read up about it, watch the catch up clip of last nights episode and be there next Tuesday at 9pm, BBC1!

MySQL 4.x to Oracle Notes

2007-10-11T00:00:00+01:00

Stumbled across this useful page full of examples and notes on how MySQL 4.x and Oracle differ, and how you can avoid complications if you want to migrate a database between the two…

About once a year I need to migrate a medium-sized web application using MySQL to Oracle.

Usually it’s to prepare a successful intranet application for a move to a formally supported production environment – and in Silicon Valley, that usually means Oracle.

I was apologizing to Monty at OSCON this year about my latest migration project away from MySQL.

His surprising response was, “It’s not a bad thing. I don’t mind hearing about conversions because successful migrations demonstrate that people don’t have to worry about database lock-in.”

Here’s some notes on doing migrations.

Adding/Deleting Rows In TableKit Tables

2007-10-11T00:00:00+01:00

This post has now been updated. Please head over to the new post for something better...

Following on from my previous post on how to integrate the excellent TableKit into your Catalyst webapp (to make your data tables dynamically editable), here’s how i’ve gone about adding ajax inserts and deletes so that you can add and remove data rows in your tables.

You’ll need the code from the previous post to follow along.

We’re going to be using prototype to do the background ajax calls, as this is already in our app as a requirement of TableKit. Now let’s get on with doctoring our template. First we add in a delete button for each row of our table. Open up /root/src/users/list.tt and change the code of our table to look like the following (the changes come on lines 9, 17, 20 and 26-28):

<table id="users" class="sortable resizable editable">
  <thead>
    <tr>
      <th id="id" class="sortfirstasc noedit">Id</th>
      <th id="firstname">First Name</th>
      <th id="lastname">Last Name</th>
      <th class="noedit nocol"></th>
    </tr>
  </thead>
  <tfoot>
    <tr>
      <th>Id</th>
      <th>First Name</th>
      <th>Last Name</th>
      <th class="nocol"></th>
    </tr>
  </tfoot>
  <tbody id="user_body">
  [% FOREACH user IN users -%]
    <tr id='[% user.id %]'>
      <td>[% user.id %]</td>
      <td>[% user.firstname %]</td>
      <td>[% user.lastname %]</td>
      <td class="nocol">
        <a class="delete" href="#" onclick="userDelete([% user.id %]); return false">delete</a>
      </td>
    </tr>
  [% END -%]
  </tbody>
</table>

The above code adds a ‘delete’ link into each row of the table. This link is to run a short javascript function (called userDelete) that we shall add now at the bottom of the template (within the original javascript block):

userDelete = function( user_id ) {
  var answer = confirm('Are you sure you want to delete this user?');
  if (answer) {
    new Ajax.Updater( 'user_body',
      '[% c.uri_for('/users/_delete_user/') %]?user_id=' + user_id,
      { asynchronous: 1, }
    );
    return false;
  }
}

This function basically asks the user to confirm that they want to delete the user entry, the sets up an Ajax.Updater that passes the user_id to be deleted to a new function in our controller (that we shall write next) which deletes it, and then passes the new table body back to be updated on screen. Let’s now create a new function _delete_user (and a helper function __return_all_users) in our user controller /lib/MyApp/Controller/Users.pm:

=head _delete_user

Ajax method to delete users from the users table

=cut

sub _delete_user : Local {
  my ($self, $c) = @_;

  # Look-up our user entry
  my $user = $c->model('MyAppDB::Users')->find({
    id => $c->req->params->{user_id}
  })->delete();

  my $output = __return_all_users( $self, $c, 'null' );

  unless ( $output ) {
    $output = '<tr><td colspan="4" class="nocol">All Users Deleted</td></tr>';
  }

  $c->res->body( $output );
}

=head2 __return_all_users

Private method for the Users ajax interaction.
Returns the inner body of a html table.

=cut

sub __return_all_users : Private {
  my ( $self, $c, $new_user_id ) = @_;

  my @users = $c->model('MyAppDB::Users')->all(
    { order_by => 'id ASC' }
  );

  my $html;
  for ( my $i = 0 ; $i < scalar(@users) ; $i++ ) {
    my $class;

    if ( $new_user_id && $users[$i]->id == $new_user_id ) {
      $class = 'new';
    } else {
      if ( $i % 2 == 0 ) { $class = 'rowodd'; }
      else { $class = 'roweven'; }
    }

    $html .= "<tr class=\"" . $class . "\" id=\"" . $users[$i]->id . "\">
      <td>" . $users[$i]->id . "</td>
      <td>" . $users[$i]->firstname . "</td>
      <td>" . $users[$i]->lastname . "</td>
      <td class=\"nocol\">
        <a class=\"delete\" href=\"#\" onclick=\" userDelete("
        . $users[$i]->id . "); return false\">delete</a>
      </td>
      </tr>";
  }

  return ( $html );
}

The _delete_user function, takes the user_id that we sent to it, deletes the entry from the database, then calls the __return_all_users function to rebuild the table body. This table body is then used to update the table back on the web page.

That’s the delete functionality sorted, now on with the row adding… Back in the template, add we add another Ajax.Updater link below the table:

<br />
<a class="add" href="#" onclick="
  new Ajax.Updater( 'user_body',
    '[% c.uri_for('/users/_add_user') %]',
    { asynchronous: 1, }
  ); return false ">add a user</a>

And add another new method into our controller to add a new user into the database and table:

=head _add_user

Ajax method to add users to the users table

=cut

sub _add_user : Local {
  my ($self, $c) = @_;

  # create a new user...
  my $new_user = $c->model('MyAppDB::Users')->create(
    {
      id        => $c->req->params->{user_id},
      firstname => '[First Name]',
      lastname  => '[Last Name]'
    }
  );

  my $output = __return_all_users( $self, $c, $new_user->id );

  $c->res->body( $output );
}

This function, like the delete function, does its business on the database, then rebuilds the table body and sends it back to the web page.

The final icing on the cake, is a little addition to our CSS to make this all look a little nicer. Open up /root/css/myapp.css and add the following to the bottom of the file:

.nocol, th.nocol {
  background-color: #fff;
  border: none;
}

tr.new {
  background-color: #ff9697;
}

a {
  outline: none;
}

a.add, a.delete {
  background: url('/images/add.png') left center no-repeat;
  padding: 2px 0 2px 20px;
}

a.delete {
  background: url('/images/delete.png') left center no-repeat;
  left: 0;
}

tr a.delete {
  font-size: 0.8em;
}

And there you go. Now you can edit, add and delete users to your database and table without having to reload the page.

However, there is one small bug that needs to be squashed to make this perfect… TableKit caches the tables on page load – if you have a go at re-sorting one of the tables after deleting or adding a row, this causes the table to essentially double in size as the original cached data is reloaded onto the screen! :( I now need to figure out a way to clean out the cache for the current table and re-initalise TableKit. Any suggestions would be more than welcome! :)

The files used in the examples can be downloaded below.

Attached Files:

MyApp – v2

Some Useful Catalyst Tips

2007-10-10T00:00:00+01:00

Found this small selection of tips that can come in use whilst working with Catalyst…

Multi-Safari and IE

2007-10-10T00:00:00+01:00

Useful tools for when you’re web developing… Been using the Multi-IE for a while, but now some bright chap has made it possible to run multiple versions of Safari on your Mac.

X-Wing Launches, Falls Apart...

2007-10-08T00:00:00+01:00

Oh dear, the rocket-powered X-Wing that was revealed last week never made it past launch day… It did get off the ground quite impressively though.

Here’s a video of the launch. :D

Accidental Caps Lock Protection On Your Keyboard

2007-10-08T00:00:00+01:00

I’ve just got one of the new Apple wireless keyboards. I have to say – i’m very impressed with it! It’s incredibly thin, good to look at, and doesn’t seem to gather as much crap in it as the old Apple keyboard. :)

Little did I know that it’s even quite smart about people hitting the caps lock key by accident. I like it even more now (as I do hit the caps lock key quite a lot by accident)!

But I did notice something odd. I rarely use the Caps Lock key, but often accidently bang it, missing the left Shift key. I would feel the mistake while typing, but then I’d look down and see Caps Lock hadn’t been engaged after all. Oh, I must have just imagined my mis-strike.

Over the next few weeks, this kept happening to the point where I started questioning reality. I was positive I hit it. This required scientifical investigation.

NodeBox

2007-10-05T00:00:00+01:00

A very interesting looking app. Some of the example images in their gallery look fantastic!

NodeBox is a Mac OS X application that lets you create 2D visuals (static, animated or interactive) using Python programming code and export them as a PDF or a QuickTime movie. NodeBox is free and well-documented.

Log/Audit Tables In Oracle

2007-10-05T00:00:00+01:00

One of the useful things that i’ve been asked to set-up lately is automatic logging of changes to several of our database tables.

My first thought was to do this in Perl (as the rest of the system is in Perl), but this would mean adding extra methods and calls in the Perl code to update the database (both the original tables and the new log tables). That seemed like a solution – a pain in the arse to implement, but a solution.

Thankfully one of the helpful chaps in my department suggested doing it all in the database with triggers as this is quite common in banks and the like. What a damn fine idea! Only a little SQL to write and no extra Perl.

Here’s an example…

First, here’s the table that we want to create an audit log for:

CREATE TABLE "COMMENT" (
  "COMMENT_ID" NUMBER(10,0) NOT NULL,
  "COMMENT_BODY" VARCHAR2(1000),
  "USER" VARCHAR2(100),
  "CREATED_DATE" DATE,
  CONSTRAINT "PK_COMMENT" PRIMARY KEY ("COMMENT_ID")
);

Now, we create the audit table – the audit table is exactly the same as the table that we wish to keep a log of, except for one extra column, “AUDIT_DATE”, this will keep record the date/time of when an change occurred on the original table.

CREATE TABLE "COMMENT_AUDIT" (
  "COMMENT_ID" NUMBER(10,0) NOT NULL,
  "COMMENT_BODY" VARCHAR2(1000),
  "USER" VARCHAR2(100),
  "CREATED_DATE" DATE,
  "AUDIT_DATE" DATE DEFAULT SYSTIMESTAMP NOT NULL
);

Finally, we create the trigger to keep a log of changes to our original table.

CREATE OR REPLACE TRIGGER "TA_COMMENT"
before update or delete on COMMENT for each row
begin
if deleting or updating then
  insert into comment_audit(
    COMMENT_ID,
    COMMENT_BODY,
    USER,
    CREATED_DATE
  )
  values (
    :old.COMMENT_ID,
    :old.COMMENT_BODY,
    :old.USER,
    :old.CREATED_DATE
  );
end if;
end;
/
ALTER TRIGGER "TA_COMMENT" ENABLE;

Now whenever a delete or update action is performed on the “COMMENT” table, a record of the old values and the date/time at which they were changed is recorded in the audit table.

Rocket-Powered X-Wing Model!

2007-10-04T00:00:00+01:00

oh. my. god. :D

This is what happens when nerds have waaay too much time on their hands. Will be great to see if this thing actually gets off the ground though! On October 10th we’ll either have our first ‘real’ X-Wing or one very crispy model of R2-D2!

Google Maps For Mobiles

2007-10-04T00:00:00+01:00

Dammit! This would have been VERY useful to know about last weekend whilst I was lost looking for a mates house in Bedford (and being quite late for the house warming party)…

Auto-Increment ID's In Oracle

2007-10-04T00:00:00+01:00

This is old news to most people who have been using Oracle for a while, but to me this is something new that I learnt today. How to have MySQL like “auto-increment” id’s for your tables in Oracle. :) Here’s an example…

First we need to create a sequence for the ID’s:

CREATE SEQUENCE "S_COMMENT_ID"
START WITH 1
INCREMENT BY 1
CACHE 10;

Then we create the table and the required trigger:

CREATE TABLE "COMMENT" (
  "COMMENT_ID" NUMBER(10,0) NOT NULL,
  "COMMENT_BODY" VARCHAR2(1000),
  "USER" VARCHAR2(100),
  "CREATED_DATE" DATE,
  CONSTRAINT "PK_COMMENT" PRIMARY KEY ("COMMENT_ID")
);

CREATE OR REPLACE TRIGGER "TR_COMMENT_ID"
BEFORE INSERT
ON COMMENT
REFERENCING NEW AS NEW OLD AS OLD
FOR EACH ROW
BEGIN
  if(:new.comment_id is null) then
  SELECT S_COMMENT_ID.nextval
  INTO :new.COMMENT_ID
  FROM dual;
  end if;
END;
/
ALTER TRIGGER "TR_COMMENT_ID" ENABLE;

And there you go – an auto-incrementing primary key… Damn that’s a lot more code to write than a simple ‘auto-increment’.

Edit: An alternative when using SQL Developer is to create your table, select it, then go to the ‘Triggers’ tab. In there you will find a useful ‘Actions…’ button where you can create a new trigger linking your tables primary key to a sequence.

F1 Got Exciting!

2007-10-01T00:00:00+01:00

Wow! I’ve been an F1 fan for quite some time, but over the last few years it’s become quite dull. Thank goodness for this year!

Nothing like some rain to bring on the fun in Japan! :D

My Halo 3 Profile

2007-09-30T00:00:00+01:00

I never knew that so many damn stats were taken from each game!

Pixelmator Released

2007-09-25T00:00:00+01:00

The new image editing app come Photoshop contender for OS X got its full release today. I have to say that it does look very good, and at only $59 (less than 30 of our shiny british pounds) any license of Photoshop (even student ones) are looking way over priced! Will have to give it a go when I get started on some new project.

Pixelmator Team today released Pixelmator 1.0, GPU-powered image editing tool that provides everything needed to create, edit, and enhance still images.

"After two months of bug squashing we are very excited to finally release Pixelmator," said Saulius Dailide of the Pixelmator Team. "With its use of latest Mac OS X technologies, breakthrough ease-of-use, innovation and low $59 price tag we think all Mac users will find Pixelmator very useful and fun."

One Day To Go...

2007-09-25T00:00:00+01:00

Yay! Halo 3 is out tomorrow and getting good reviews. I think i’d better get ready to rush into my local Game at some point tomorrow!

From a certain point of view, Halo 3 is without a doubt the biggest game of the year. The combination of fan anticipation, marketing, and the skill of Bungie’s design combine to create a game that’s larger than life; if gaming has a blockbuster franchise to match the movie industry’s punch, it’s the tale of Master Chief. The importance of the Halo franchise to gaming is a very big issue, though, and one worth it’s own article. Having played through the game, there’s really only one question I’m here to answer today. Does it meet expectations? In a word: yes. It’s not the best game ever made, and it may not even be the best game this year. Will it make the fans happy, and deservedly sell thousands of Xbox 360s? Very much yes.

Making Editable Tables with Catalyst and TableKit

2007-09-23T00:00:00+01:00

Catalyst is an MVC web-development framework for Perl, very similar in concepts, ideas (and even some of the implementation) to Ruby on Rails. I’m using Catalyst a lot in my job now, and one of the first challenges that i’ve had to go through is making dynamically editable tables for some of the views we are using (in other words, Ajax driven edit-in-place tables).

Following a short Google, there seemed to be only two ready-made options I could see: one, using the Catalyst controller module Catalyst::Controller::ROSE::EIP; or two, by integrating and using the stand-alone javascript package TableKit.

Unfortunately the first option, ROSE::EIP is dependent on the use of the Rose::DB::Object as your database ORM mapper. As our webapp is already using DBIx::Class as its ORM layer, that rules ROSE::EIP out and TableKit was the way to go. Here’s a quick rundown of how I got it going, using a very simple table to store a users first and last names as an example (all files used in this tutorial are available for download at the bottom of this post) and a single controller called ‘users’.

First off, head on over to the TableKit site and download the latest TableKit package, then create the following three directories in your /MyApp/root/ directory: javascript, css, and images.

From the TableKit download, copy the files: tablekit.js, fastinit.js and prototype.js (found in scriptaculous/lib) into your new ‘javascript’ directory; then copy the two images – down.gif and up.gif into the images directory.

Now create a new file and add in the following CSS code:

table {
  border-collapse: collapse;
}

td, th {
  padding: 0.5em;
  border: 1px solid #CCC;
}

thead, tfoot {
  background-color: #DDD;
}

thead {
  border-bottom: 2px solid #f08900;
}

tfoot {
  border-top: 2px solid #f08900;
}

tr.rowodd {
  background-color: #FFF;
}

tr.roweven {
  background-color: #F2F2F2;
}

.sortcol {
  cursor: pointer;
  padding-right: 20px;
  background-repeat: no-repeat;
  background-position: right center;
}

.sortasc {
  background-color: #DDFFAC;
  background-image: url('/images/up.gif');
}

.sortdesc {
  background-color: #B9DDFF;
  background-image: url('/images/down.gif');
}

.nosort {
  cursor: default;
}

th.resize-handle-active {
  cursor: e-resize;
}

div.resize-handle {
  cursor: e-resize;
  width: 2px;
  border-right: 1px dashed #1E90FF;
  position:absolute;
  top:0;
  left:0;
}

Save this file as ‘myapp.css’ in your new css directory. This will give your tables a on okay looking starting point and nice striping on odd and even rows when we’re finished.

Next, open up the /MyApp/root/lib/site/html file and add the following lines within the head tags:

<link href="/css/myapp.css" rel="stylesheet" media="screen" type="text/css" />
<script src="/javascript/prototype.js" type="text/javascript"></script>
<script src="/javascript/fastinit.js" type="text/javascript"></script>
<script src="/javascript/tablekit.js" type="text/javascript"></script>

Now, we update our /MyApp/root/src/users/list.tt file so that the users table looks like the following snippet of code:

[% META title = 'User List' -%]
<table id="users" class="sortable resizable editable">
  <thead>
    <tr>
      <th id="id" class="sortfirstasc noedit">Id</th>
      <th id="firstname">First Name</th>
      <th id="lastname">Last Name</th>
    </tr>
  </thead>
  <tfoot>
    <tr>
      <th>Id</th>
      <th>First Name</th>
      <th>Last Name</th>
    </tr>
  </tfoot>
  <tbody>
    [% FOREACH user IN users -%]
    <tr id="[% user.id %]">
      <td>[% user.id %]</td>
      <td>[% user.firstname %]</td>
      <td>[% user.lastname %]</td>
    </tr>
    [% END -%]
  </tbody>
</table>

In the above lines of code there are two important details that need to be done in order for the table sorting and editing to work:

One: The id properties

The id properties on each column of the table are set to the same names as the fields in the database table. and the table rows, (in the body of the table) also have an id associated with them – this becomes the database row ‘ID’ attribute when the template is interpreted. These id’s then become some of the parameters that are passed via TableKit to our Ajax.Updater controller method.

Two: The class properties

In the table header, the id column has two classes applied to it – ‘sortfirstasc’ and ‘noedit’ – this tells TableKit to first sort the table based on this column (and ascending), and that the values of this column are not to be editable.

Also in the declaration of the table, the table has the classes: ‘sortable’ ‘resizable’ and ‘editable’ – these tell TableKit what you’d like to be able to do with your table.

Finally, add the following snippet of Javascript code to the bottom of the same file (/MyApp/root/src/users/list.tt):

var comments_table = new TableKit( 'users', {
  editAjaxURI: '[% update_uri %]'
});

This initializes the TableKit actions and tells TableKit the uri that the Prototype Ajax.Updater is to call (a Catalyst controller method that we’re about to create).

The final step is now back in the ‘Users’ controller. Here’s the code that we need for both the initial list of users and the Ajax.Updater method that TableKit calls:

sub list : Local {
  my ($self, $c) = @_;
  $c->stash->{users} = [$c->model('MyAppDB::Users')->all];
  $c->stash->{template} = 'users/list.tt';
  $c->stash->{update_uri} = $c->uri_for('/users/_update_user');
}

sub _update_user : Local {
  my ($self, $c) = @_;

  $c->model('MyAppDB::Users')
    ->find({ id => $c->req->params->{id} })
    ->update({
      $c->req->params->{field} => $c->req->params->{value}
    });

  $c->res->body( $c->req->params->{value} );
}

There you go, you should now have a table on your ‘/users/list’ page that is sortable, resizable, and now even in-place editable. I hope these instructions are clear enough (there’s quite a lot in there!), any questions, comments or improvements people could give me would be most appreciated.

Next up, i’ll go through how I made the tables more functional by adding in add and delete buttons (to add and delete rows to the table, and therefore create new database entries). :)

Attached Files:

MyApp

At Last! iCal To Show Correct Date!

2007-09-23T00:00:00+01:00

This makes me happy…

One final note: It looks like Leopard’s iCal dock icon displays the proper date at all times! The dozen or so people who have clamored for this may rejoice.

Macs Really Do Run Windows Better

2007-09-22T00:00:00+01:00

Oh so very true…

Ever since Boot Camp appeared on the scene, there have been several comments about Macs being better Windows machines than Windows machines. The weird thing is it’s actually true.

Let's get started...

2007-09-11T00:00:00+01:00

Welcome to the introductory post to hocuspokus.net! So, what’s going on here then?!?

Well, basically this is going to be a place for me, Darren Oakley to dump my thoughts and little ideas that I have on a semi-regular basis… Expect posts on subjects such as Apple (god – not another mac blogger!), Perl programming, Bioinformatics (it’s what I do for a living), Unix geekiness, Xbox 360 and many things in between as I go about my daily life.

Anyway – enough of this boring first post nonsense! Will be back soon with more interesting things to say!