However, for FuncNet we have a simple script running in a cron job, which posts a status message to @FuncNet every so often. This runs without any supervision, so I was left scratching my head as to how I could obtain the access token and access token secret required to post. The app registration page at http://twitter.com/oauth_clients/details/NNNNNN for each app only shows its consumer key and consumer secret which are something different.

Eventually, thanks to Net::Twitter developer Marc Mims on this thread, I discovered that there’s a whole separate page for each app at http://dev.twitter.com/apps/NNNNNN/my_token which has the access token and access token secret required for the app to post to its own account.

N.B. In the URLs above, NNNNNN corresponds to the numeric ID for your application. If you don’t know what this is, just go to http://dev.twitter.com/apps, click on the app name to get the consumer strings, and then click on My Access Token to get the access strings.

Once you have these, you can post like this (thanks again to Marc for example):

    use Net::Twitter;
 
    my $nt = Net::Twitter->new(
        traits => [qw/OAuth API::REST/],
        consumer_key        => $YOUR_CONSUMER_KEY,
        consumer_secret     => $YOUR_CONSUMER_SECRET,
        access_token        => $YOUR_ACCESS_TOKEN,
        access_token_secret => $YOUR_ACCESS_SECRET,
    );
 
    $nt->update("Bob's your uncle!");

Why you need 4 distinct incomprehensible strings in order to post a single tweet, I don’t know, but presumably it’s justified on security grounds. What isn’t justified is Twitter hiding two of them somewhere else entirely, and not linking to that place from the main OAuth page for the app.

Not useful, guys.

UPDATE: It seems there are bigger problems with Twitter’s new process. This detailed ArsTechnica article describes OAuth 1.0a as “an inelegant hack” and Twitter’s implementation of it as being “against all reason”.

If you’re having trouble with it, you’re not alone; it seems almost designed to cause problems for app developers, and particularly open-source app developers. The article’s well worth a read.

Thankfully, the solution was easier than I thought. Do all the following as root…

1. Install dpkg, the Debian package management tool:

yum install dpkg

2. Download the base package for your architecture, and the gnome support package, from here:

http://repository.spotify.com/pool/non-free/s/spotify/

3. Create a temp directory, and unpack them there (we want to check for clashes):

mkdir spotify
cd spotify
dpkg -x ../spotify-client-qt_0.4.7.132.g9df34c0-1_amd64.deb .
dpkg -x ../spotify-client-gnome-support_0.4.7.132.g9df34c0-1_all.deb .

4. This gives you a directory tree starting at /usr. You can check for clashes like this:

find -not -type d -exec ls -l /'{}' \;

… and make sure there’s no files found.

5. Then re-extract them into your root partition (hence checking for clashes first):

dpkg -x ../spotify-client-qt_0.4.7.132.g9df34c0-1_amd64.deb /
dpkg -x ../spotify-client-gnome-support_0.4.7.132.g9df34c0-1_all.deb /

6. Finally, we need to manually install qt-x11 as this dependency is needed:

yum install qt-x11

7. Then just type spotify and log in!

Seems pretty stable so far, apart from a couple of minor glitches.

EDIT: As suggested by Tyson Key in this thread, I got rid of the audio glitches by starting the PulseAudio volume control (/usr/bin/pavucontrol) before Spotify. Maybe this adds some buffering or something.

N.B. I take no responsibility if this process damages your computer, your music collection, your hearing or your sanity. Try at your own risk

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

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

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

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

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

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

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

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

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

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

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

They’ve finally (after nearly six years) added the ability to temporarily turn the code formatter off for a tricksy block that needs its own custom formatting. e.g.:

			// @formatter:off
			xml
			.append( "<node id='" )
			.append( protein )
			.append( "'><data key='class'>" )
			.append( cls )
			.append( "</data><data key='label'>" )
			.append( protein )
			.append( "</data></node>" );
			// @formatter:on

See the Off/On Tags tab for details.

Nice one guys… Eventually.

We have a special guest this month, Cameron Neylon, with an open-science-themed talk entitled “What have the public done for us?” Plus lightning talks on various subjects.

In other news, I’ve moved the blog over to the much cleaner and airier Barthelme theme. Drop a comment if it gives you any problems.

This month’s speakers:

Catherine Canevet — Ondex: Data integration and visualisation

Christopher Barnes — ABC-SysBio: Approximate Bayesian Computation in Python with GPU support

N. Purswani, L. Tweedy, Z. Patel, C. Suriel-Melchor — DASbrick: A cloud based Rich internet application for Synthetic Biology Parts Registries

Does anyone have a link for DASbrick?

Drinks afterwards at Imperial’s Eastside Bar. See the BioGeeks blog for full details.

#!/bin/bash
export MYSQL_PWD=myrootpassword
BACKUP_DIR=/mnt/backups/mysql_backups
DATE=`date -I`
for dbname in `mysql -uroot --batch --skip-column-names -e "show databases;" | grep -v information_schema`; do
	/usr/local/bin/mysqldump -u root $dbname | gzip -9 > $BACKUP_DIR/$dbname-$DATE.sql.gz
done
 
# Clear backups older than 7 days
/usr/local/bin/find $BACKUP_DIR/*.sql.gz -mtime +7 -delete

Edited to include compression. Remember to include full paths if you’re running it from a crontab, just in case.

Chris Staite from the University of Birmingham has built a statically-linked version of Chromium, the open source version of Google’s Chrome browser, for Centos.

You can get it from here.

I was getting so sick of Firefox’s slowness and bloat, and Chromium is so much snappier, and more memory-efficient too.

Although to be fair, I don’t have nearly so many extensions installed yet…

It should just work out of the box with no extra dependencies to install. I’m using 64-bit Centos 5.4, and although it’s a 32-bit app, it seems entirely happy so far.

The distribution of votes across the parties correlates very badly with the distribution of seats they get in return.

It’s possible, and not uncommon, for a party’s overall vote share to go down and yet its parliamentary influence to go up, or vice versa.

After years of adversarial flip-flopping, the system’s thrown up a result which nobody seems to be satisfied with, regardless of their party affiliation. (Except maybe the Greens )

There are electoral reform demonstrations happening tomorrow, in London and all across the country:

http://www.takebackparliament.com/

If you can spare a few hours to go along, hopefully we can get a good turnout and make the case for real change while it’s still very topical — not the waffly kind of change that politicians promise every time and never deliver.

I’ll be in Trafalgar Square from 2pm.

Andrew.

We have talks from…

Alison Cuff, UCL

The CATH database — Structural Diversity and the Question of the Fold Continuum

Andrew Martin, UCL

SAPTF — Sequence Analysis Plugin Tool Framework

John Pinney, Imperial College

GLASS — Gene LAyout by Semantic Similarity

Followed by drinks at 7:30-ish at the College Arms.

Full details, maps, directions etc. are on the BioGeeks blog.