UPDATE: posted my workaround code below, good feedback already from Ryan (djatoka dev) and I’ll be testing the proper fix on the server soon.
I’ve got a server that keeps filling up its disk space and failing to serve images after it gets to the file system full error message.  First of all let me say, I don’t blame it in the least, if the admin (aka me) doesn’t do enough to secure the server enough disk space to do its job, I say, let me have it.  But after I’ve set the suspect daemon to use a *reasonable* amount of space I stopped thinking of it as the culprit, so when this issue arose again, I looked elsewhere for the cause.  Fast forward to today, the server’s file system filled up again, and refused to serve any more data, again, I totally understand where the server is coming from, if it doesn’t have enough disk space to do its job, it shouldn’t have to apologize to anyone; it’s all on the admin (again, aka, me), but what was going on? So, after I finally figured things out, I was/am still a bit confused here, but to my defense, when I did an ‘ls -ltrs /tmp’ to look at directories of old cached files left over by adore-djatoka (which is the JPEG2000 (J2K) image server that I suspected of taking up all the disk space) :

# ls -ltrs /tmp | grep temp-20090519-*
5.7M drwxr-xr-x 2 tomcat55 root     5.7M 2009-05-19 13:08 temp-20090519.130841

I concluded that the adore-djatoka server was innocent, and I felt bad for accusing it of the infraction since the largest directory I’d come across that it was responsible for was a paltry 5.7M.  Immediately I thought to myself, “…these are not the droids you’re looking for“, after all, this couldn’t be responsible for a directory that was taking up almost 100G and making me look like a sophomore taking the “Intro To Computers” class for the second time, right?  But finally I got an unbiased opinion when I found a Unix utility called ncdu, which is an NCurses Disk Utility (du is an old school Unix utility which displays ‘disk usage’ of a selected directory), that, when run against the same directory as I scanned before, told me:

# ncdu /tmp | grep temp-20090519-*
70.5GB [##########] /temp-20090519.130841

Now look, I’m no math wiz, but come on, WTF am I seeing wrong here?

[...]

So, long story short, the ncdu utility is able to delete the Gigs worth of files much quicker than my script, so the server now has plenty of disk space, and I now have a rotate script that I humorously call tomcat_turnover that will:

1. rotate out the old Tomcat temp directory (which is where the adore-djatoka server stores its cached images)
2. create a new Tomcat temp directory
3. set the proper permissions on the new Tomcat temp directory
4. restart Tomcat (and thus the adore-djatoka server)
5. and finally, delete the contents of the old Tomcat temp directory, thus returning that used disk space to free disk space once again

So, now tell me why is this “my problem” and not instead handled by the sever, and why doesn’t the adore-djatoka server respect the settings I set in djatoka.properties?

# grep cache /var/lib/tomcat5.5/webapps/adore-djatoka/WEB-INF/classes/djatoka.properties
OpenURLJP2KService.cacheEnabled=true
#OpenURLJP2KService.cacheTmpDir=
OpenURLJP2KService.cacheSize=1000
OpenURLJP2KService.cacheImageMaxPixels=100000

Now, assumming cacheSize=1000 doesn’t stand for 1000Gig, I’ve either found a bug in the djatoka software, which I’ll post a bug report to the project to determine, or this is an error by the well meaning admin (aka me). More info when I learn about it, and yes, I’ll post my tomcat_turnover script here for extra credit next
The tomcat_turnover.sh workaround code:

# wrapper to recycle tomcat, while taking care to clean the old
# temp directory independantly of restarting tomcat.

APP=”tomcat5.5″
GROUP=”root”
DIR=”/var/lib/${APP}/temp”
DATE=.`date +%Y%m%d.%N`

# stop tomcat
/etc/init.d/${APPILCATION} stop

# shuffle directories
mv ${DIR} /tmp/temp${DATE}
mkdir ${DIR}
chown -R ${APP}:${GROUP} ${DIR}

# restart tomcat
/etc/init.d/${APPILCATION} start

# clean old temp
cd /tmp
nice -n 19 find temp${DATE} -atime 1 | while read x
do
rm $x
done
rm -rf temp${DATE}

# done
exit 0

While looking for something else, (which is mainly when I find *other* interesting things) I found an article which included links for four free Linux eBooks. This is a great resource for anyone with some Linux experience, back to others who may be looking to get started with tux, and I would have loved to have this when I started, but that was before the Internet was available to most people. So, if you’re new to Linux, or want to get started (I used Red Hat Unleashed in 1996, here it is online!), here’s some great downloads to learn from:

Linux Starter Pack

By TuxRadar

Here’s your complete guide to using Linux, taking you from beginner level to an intermediate user with ease. This ebook will show you how to install Linux, navigate around the desktop, use common software, add more programs and fix any problems you may encounter. It’s based around a slightly older version of Ubuntu Linux so there may be some minor differences with newer releases, but you can always download the latest version from www.ubuntu.com or get a CD sent by post at shipit.ubuntu.com.

The Linux Starter Pack (PDF) 11.5MB

The Easiest Linux Guide You’ll Ever Read

by Scott Morris
After several months of writing and revising, Scott has made available the “Easiest Linux Guide You’ll Ever Read”. It is a 160-page book geared towards people who are competent with using Windows, who have never attempted to use Linux but are interested in giving it a try. This ebook seems to be around for quite some time, so I wouldn’t be surprised if a lot of you have already went through this copy. For a more thorough review of this ebook, click here, or click on the link below to grab it.

The Easiest Linux Guide You’ll Ever Read (PDF) 5.66MB

SUSE Linux Administration Guide

Too many authors to be listed here
The SUSE LINUX Administration Guide provides background information about the way your SUSE LINUX operates. This book introduces Linux system administration basics such as file systems, kernels, boot processes, an Apache web server, and secure authentication.

SUSE Linux Administration Guide (HTML)

Ubuntu: Pocket Guide and Reference

A concise companion for day-to-day Ubuntu use
by Keir Thomas
A comprehensive, 170 page ebook which will get you started with Ubuntu. I believe a lot of computer users have intentions of getting a Linux system up just to test and experience the power behind this free operating system. There are various types of Linux, but so far, and at least for me, Ubuntu seems the most popular so far. I’m no means an experienced user of Ubuntu, so I can’t really speak on why it’s popular, but I think the simplicity, compatibility and user friendliness should do the trick. Some of the chapters in this ebook include:-

• Introduction
• Chapter One: Installing Ubuntu
• Chapter Two: Configuring Ubuntu
• Chapter Three: Getting to grips with the desktop
• Chapter Four: Users and the filesystem
• Chapter Five: Hands-on at the command-line
• Chapter Six: Software management
• Chapter Seven: Securing the system

Ubuntu: Pocket Guide and Reference (PDF) 2MB

Recently I’ve been looking at ways to solve some of biodiversities’ long standing issues with LSIDs, which are, “Life Science Identifiers are a way to name and locate pieces of information on the web. Essentially, an LSID is a unique identifier for some data, and the LSID protocol specifies a standard way to locate the data (as well as a standard way of describing that data). They are a little like DOIs used by many publishers.“  I posted my thoughts to the TDWG discussion mailing list on the topic, and am reprinting it here to allow for further community commentary; Code4lib, I’m looking at you. While much of it is theoretical, it is doable, and if it covers all that needs to be addressed, would be a cool, sustainable way forward for link resolvers for all kinds of usage.

I’m with Tim on this one, and taking one of Rod’s other posts (”LSIDs, disaster or opportunity“) a bit further, I think coming up with a simple, extend-able URL resolver would give us many benefits and allow LSIDs with extra, added information around them for all to use. Looking at his example, a URL would get permanent tracking that would also post referrers, location and traffic. A summary of the link could even be a page in itself, a cached version, a screenshot, or just a scrape of the code – pulling out the HTML tags, for future reference in case the real link goes down. We could use the ability to create a customizable prefix (ie- http://someresolvr.com/bhl/SDFoijF), to somewhat follow DOI conventions, but could even save old DOIs or handles for historical purposes in a field attached to the new URL, or for reuse, making the new URL resolve to a current DOI with a simple post at the end of the new URL (ie- http://someresolvr.com/bhl/SDFoijF/DOI). In the same way we could use user input, data pulled about the URL semantically to generate RDFa (by using pyRdfa), then exposing that for all newly created URLS, and coming up with a standard to make it predictable (ie- http://someresolvr.com/bhl/SDFoijF/RDF). The example at bit.ly shows the use of Open Calais to get more background information on the original link to provide more information, but it could also be pointed to other services we provide/use in biodiversity to provide a snapshot across the board of more context/content. Users of the service could login to examine/add/edit the data by hand if desired, so they would still retain ultimate control over how their record is presented. Thus, from a simple URL, we could build a complete summary that would build on what we’re given while sharing it all back out.

Then the architecture (aka, the fun part) would be simple and distributed. A webserver able to process PHP, running the database CouchDB would be all that is needed to run the resolver. CouchDB is schema-less, so the way it handles replication is very simple, and is built to be distributed, only handing out the bits that have changed during replication, as well as scale in this manner. Having a batch of main servers behind a URL in a pooled setup (think of a simplified/smaller version of the Pool of Unix networked time servers) would allow a round-robin DNS, or a ucarp setup (”urcarp allows a couple of hosts to share common virtual IP addresses in order to provide automatic failover“), so if one main server went down, another would automatically take over, without the user needing to change the URL. Plus, if we wanted to, to battle heavy usage of the main servers we could use the idea of Primary and Secondary servers as outlined in the pool.ntp.org model, so an institution with heavy usage could become a Secondary host and run their own resolver simply, with almost no maintenance. They would just need the PHP files, which would be a versioned project, and then have a cron task to replicate the database from a pool of the main servers. The institution’s resolver could be customized to appear as their own, (ie- http://someresolvr.bhl.org/bhl/SDFoijF) and for simplicity could be read-only. This way a link like http://someresolvr.com/bhl/SDFoijF could be resolvable against any institution’s server, like http://someresolvr.bhl.org/bhl/SDFoijF or http://someresolvr.ebio.org/bhl/SDFoijF – as all of the databases would be the same, although maybe a day behind, depending on the replication schedule. New entries would only be entered on a main server, or in ‘the pool’ (ie- http://pool.someresolvr.com/), then those changes would be in the database to be handed out to all on the next replication (I won’t add my P2P ideas in this email – it may not be needed for the deltas that would need to be transfered daily or weekly). Add to all of this that CouchDB is designed as “…a distributed, fault-tolerant and schema-free document-oriented database” which would fit into what we want to do; build a store of documents (data) about a URL that we can serve, while being a permanent, sustainable resolver to the original document. If the service ever died, it could be resurrected from anyone’s copy of the database (think LOCKSS (Lots of Copies Keep Stuff Safe)), so that no data (original or accumulated) would be lost. The data could be exported from the database in XML, and then migrated from that to a desired platform.

I have not been dealing with LSIDs as long as most on this list so I expect I’m glossing over (or missing) some of the concepts, so please let me know what I am lacking. This is a needed service, and is a project I’d like to be involved in building.

The British comedy Red Dwarf has been a favorite of mine for many years, and this year it celebrates its 20th year anniversary.  While they show hasn’t *constantly* been in production this fact is a bit misleading, but regardless, this year the crew of The Cat, Rimmer, Lister and Kryten are reuniting for a new 3 part series, Back To Earth. Their previous adventures cover all sorts of ground, but basically there’s a skeleton crew left in a mining ship lost far out in space.  I’ve been in the loop on the new episodes since I’m following Robert Llewellyn on Twitter, he plays Kryten, the android on the right in the picture.  It’s been really interesting learning about the man behind the character as he goes about his day, with a lot of his efforts focused on Car Pool, an interview show he produces where he interviews celebrates while car pooling in his Prius. Really funny stuff. As a bonus, a few weeks back he had Chis Barrie, who plays Lister in Red Dwarf, as seen standing next to Kryten above.  It’s a funny interview, file those two under guys I’d like to have some beers with.  You can find the show on Robert’s own site, Llewtube or download them as podcasts over at iTunes.  For the uninitiated who are interested in Red Dwarf, the best way to start is at the end, and by the end I mean the pilot for the show entitled The End. The shows are all on DVD and hilarious, and next to AbFab I can’t think of a British Sitcom that I enjoy more.

So I’ve been using Fedora-commons for almost a year, first off, no it is NOT the Linux distribution, it is a digital repository used by libraries, museums, etc, worldwide to keep track of their digital collections.  For this Fedora-commons is very good at its job, but there was a steep learning curve when I first jumped in with, a complaint I’ve heard repeated by many who aren’t Java jockeys (just made that up).  Today I had to reinstall Fedora-commons on a new development server, and to be honest I had a couple of missteps along the way as I tried to remember my super cool moves to install this app.  Once something like this happens it’s a prime candidate for a HOWTO, so here is my super, simple HOWTO get Feodora-commons up and running in a development environment in Debian GNU/Linux (I’m running Lenny – 5.0) or Ubuntu Linux.  Notice that for simplicity’s sake, this uses Fedora-commons built in Tomcat implementation, for developing this is fine, for production I highly recommend installing a Tomcat via dpkg/apt-get, or whatever package manager you use, so that any security patches will be available for apt-get to automatically update.  I’ve also set it to use a local MySQL store, change to a different database if you need to.

1. download the latest version of Fedora-commons (my example uses wget, since that’s how I role, and is with the latest currently available version, modify as needed)

wget http://downloads.sourceforge.net/fedora-commons/fedora-installer-3.1.jar

2. create a filed called ‘install30.properties’ so you don’t have to answer all the questions the installer asks.  Read through this example and modify as needed.

# example install.properties
ri.enabled=true
messaging.enabled=true
apia.auth.required=false
database.jdbcDriverClass=com.mysql.jdbc.Driver
ssl.available=false
database.jdbcURL=jdbc\:mysql\://localhost/fedora30?useUnicode\=true&characterEncoding\=UTF-8&autoReconnect\=true
messaging.uri=vm\:(broker\:(tcp\://localhost\:61616))
database.password=secret
database.mysql.driver=included
database.username=root
tomcat.shutdown.port=8001
deploy.local.services=true
xacml.enabled=false
database.mysql.jdbcDriverClass=com.mysql.jdbc.Driver
tomcat.http.port=8080
fedora.serverHost=localhost
database=mysql
database.driver=included
tomcat.home=/opt/fedora/tomcat
fedora.home=/opt/fedora
rest.enabled=true
install.type=custom
servlet.engine=included
fedora.admin.pass=fedoraAdmin

3. create a database as defined above (NOTE: this could be different for you, if you’re not using a DB, enter database.jdbcDriverClass=com.mcoi.jdbc.Driver and remove the MySQL specfic lines)

mysqladmin -h localhost -u root -p  create fedora30

4. then run the Fedora-commons installer, using the -jar switch with Java and calling out your properties file at the end

/usr/lib/jvm/java-6-sun/jre/bin/java -jar fedora-installer-3.1.jar install.30.properties

5. to start Fedora-commons, define your FEDORA_HOME, JAVA_HOME, etc in your profile, or a simple BASH start script – here’s an example, again modify as needed.

# example start_fedora.sh
export JAVA_HOME=”/usr/lib/jvm/java-6-sun”
export FEDORA_HOME=”/opt/fedora”
export CATALINA_HOME=”$FEDORA_HOME/tomcat”
/opt/fedora/tomcat/bin/startup.sh

6. run the BASH script, watch for any errors

./start-fedora.sh

7. view the Fedora Admin within a web browser (change the URL to suit)

http://localhost.domain.com:8080/fedora/search

8. later, learn how to import stuff
9. ???
10. Profit!

Thanks goes out to all at Fedora-commons, specifically those on the mailing list that walked me through the early steps and made that learning curve just a bit flatter. I’m still planning on working on a Debian ‘deb’ installer to simplify the above process.  If you hit any questions or have issues with the above, leave a message below.

Thanks

UPDATE: read Euclid Records excellent post from last year by the owner Joe, “Record Store Day: What It Means To You and Me” for some insight into why you should care and participate in RSD
If you’re like me, you can’t wait for Record Store Day 2009. If you were with me last year, you’ll recall that I blogged about it and gave my review of it afterward – I really enjoyed walking up to Euclid Records where I saw the same old staff I’ve seen for years, along with people from the neighbor hood, a local(ish) band play (which my *kids* said were too loud (win!)) and of course picked up some new music. This year’s event will be April 18th, and you know I’m saving my pennies for the day. I think this year I’ll surprise the staff with some donuts to kick the day off right! If not for local music shops, the music world would be even less human, here’s to them rallying a comeback around the world. As, looks like this year bands and artists are seeing the value of having a day devoted to the music merchants, and are chipping in a bunch of exclusive releases to celebrate.

The organizers of Record Store Day have been happily overwhelmed by a steady flurry of support and activity from artists, record labels and retailers wishing to participate in the annual event in salutation of the independent music store. This year Record Store Day is set to feature a number of exciting new products made especially for the event from such well-known artists as Radiohead, Wilco, Tom Waits and Lucinda Williams and the Flight of the Conchords, just to name a few.

Wilco plan to release their upcoming DVD as an exclusive release to indie stores and on the band’s website on Record Store Day. The group’s Jeff Tweedy told Billboard Magazine in a recent interview, “Even if I wasn’t in a band, I’d still support Record Store Day. It’s a great thing and I’m glad we could do something special with them for our DVD.”

The Decemberists will release a Record Store Day 7″ as well. The band’s Colin Meloy adds, “I don’t know what I would do without indie record stores. Growing up in a town without them, I can tell you that it’s no fun to shop for indie records at chain box stores.”

You can also expect a slew of vinyl releases from Radiohead, My Morning Jacket who will release a CD as well as limited run double 10″ vinyl recorded live in Louisville at record store Ear X-tacy.

Also expected are classic split 7″ releases from Tom Waits and Lucinda Williams who will issue a double 7″ of live tracks from Atlanta and Edinburgh, as well as Sonic Youth exclusive Record Store Day split singles with Beck and Jay Reatard.

Other indie rock elder statesmen the Jesus Lizard will release a special package to include nine 7″ singles and Guided By Voices will re-release their Hold On Hope LP, with three bonus tracks.

And in the “legends” category, Bruce Springsteen, Bob Dylan, Leonard Cohen will all release RSD exclusive 7″ singles. Def Jam also plans to release a 4 LP gatefold history of the label, the physical version of which will be for indies only.

Fans can expect more unique Record Store Day pieces from a diverse array of artists such as Metric, Slipknot, Jane’s Addiction, The Smiths, the Stooges, MC5, Modest Mouse, Slayer, Rivers Cuomo, the Black Kids, Brandi Carlile, Taking Back Sunday, among many others.

In addition, Coachella, the world-renowned annual music festival set to take place on April 17-19 in Indio, California, has chosen Record Store Day to run the event’s popular on-site record store, with management provided by popular Southwest-based indie retailer, Zia Record Exchange. The on-site Coachella store, previously operated by Virgin, is noted for its high profile foot traffic and good vibe.

Record Store Day, April 18, 2009, coincidentally falls smack in the middle of the dazzling desert-set festival. Promoted by GoldenVoice, Coachella 2009 boasts such an eclectic mix of big name headliners as Paul McCartney, Amy Winehouse, My Bloody Valentine, Public Enemy, TV On The Radio, The Cure, The Hold Steady, Leonard Cohen, Morrissey, Jenny Lewis, Franz Ferdinand as well as many others sure to be stopping by the Record Store Day site to peruse the shelves for records and memorabilia and hang with their fans between sets.

A number of artists performing at this year’s Coachella will release product expressly for Record Store Day. Among them, Mastodon who will release “Crack The Skye” on 180 gram vinyl to include an extra 7″ single and lyric sheet, Jenny Lewis will issue a split 7″ with none other than Elvis Costello, and Black Keys will release a special RSD split 7″ with the Flaming Lips.

I have an older Röyksopp cd, and Norwegian duo has everything you could want in an electronic outfit; driving beats, unobtrusive synthesized vocals topped by happy melodies to rule them.  Of course if the video features a Space Invaders theme, it’s going to immediately get my attention, plus I love the idea of advertising attacking us, so here we are.  Am I that transparent?  Na, I think I just like some escapism from indie rock every now and then and this kind of pop is the vessel.  Looks like I have my next target to buy, and I will now surf around for the perfect Space Invader tattoo; it’s out there somewhere (uh, yeah)

While the TSA alway seem to be trying to cover every eventuality, even warning me about my 6 oz. tube of hair gel last week in Rhode Island, statistical studies are showing that racial profiling is no better than radom screening in finding terrorist suspects. Just as people with the same names as potential suspects are showing up on watchlists, this is not a good way to determine their threat level.  While there certainly are many challenges to generating profiles of potential terrorists, this study released by the Proceedings of the National Academies of Science does a mathematical analysis how we’re deploying the profiles we do have, and suggests we may not be using them wisely.

The study was performed by William Press, who does bioinformatics research at the University of Texas, Austin, with a joint appointment at Los Alamos National Labs. His background in statistics is apparent in his ability to handle various mathematical formulae with aplomb, but he’s apparently used to explaining his work to biologists, since the descriptions that surround those formulae make the general outlines of the paper fairly accessible.

Press starts by examining what could be viewed as an idealized situation, at least from the screening perspective: a single perpetrator living under an authoritarian government that has perfect records on its citizens. Applying a profile to those records should allow the government to rank those citizens in order of risk, and it can screen them one-by-one until it identifies the actual perpetrator. Those circumstances lead to a pretty rapid screening process, and they can be generalized out to a situation where there are multiple likely perpetrators.

Things go rapidly sour for this system, however, as soon as you have an imperfect profile. In that case, which is more likely to reflect reality, there’s a finite chance that the screening process misses a likely security risk. Since it works its way through the list of individuals iteratively, it never goes back to rescreen someone that’s made it through the first pass. The impact of this flaw grows rapidly as the ability to accurately match the profile to the data available on an individual gets worse. Since we’ve already said that making a profile is challenging, and we know that even authoritarian governments don’t have perfect information on their citizens, this system is probably worse than random screening in the real world.

Many say racial profiling is just another form of racism, but is it an effect of the TSA in picking out possible suspects, or a reflection on what our society sees as a threat? Either way, just as our not being able to take a big bottle of shampoo on a plane, it’s not making us any safer.