How to have an iPod without using iTunes

I trashed Brenda's iPod today. I eventually managed to recover it. Here's what happened:
I ripped a couple of CDs and copied them to the iPod using gtkpod. This was an experiment. I had always used iTunes before, but I am trying to escape from Windoze so I wanted to see if I could use some open source software on my Debian machine. I found that although the iPod contained the new music, once the iPod was supposedly synch'd then disconnected, the iPod reckoned the music wasn't there. As I tried various approaches eventually the iPod reckoned there was no music on there at all. Even doing a factory reset didn't fix it. On my travels I found stories of people who had managed to get iTunes up and running on their system using wine. That didn't work for. For a start, the Etch version of Debian has a version of wine that is too old. I tracked down a backport and I used winetricks to fool the system into thinking I am on XP, which the iTunes installer requires. But iTunes could not fix the iPod with the state it had gotten into, and IMHO iTunes is rubbish anyway.
Eventually I found out that the problem is caused by Apple turning the iPod against me. They want it to work only with iTunes and they keep revising the firmware to make it not work with other software. This is behaviour worthy of the Evil Empire itself. Brenda's iPod is a fourth generation nano. That means it has all the latest stuff to prevent people being able to use the device without using Apple software.
I found that some kind people have backported a recent version of gtkpod to Debian Etch. The glibpod3 library required has also been backported. I downloaded and installed the Debian packages. The next and final trick was to update a crucial file on the iPod which is used to identify the firewire device. I mounted the ipod to /med/ipod. This made the pathname of the file to be /media/ipod/iPod_Control/Device/SysInfo. Run the command "sudo lsusb -v | grep -i Serial" (without the "") with your iPod plugged in, this should print a 16 character long string like 00A1234567891231. This is the id. Put it in that file in the form:
FirewireGuid: 0xffffffffffffffff.
The leading '0x' is important.
I found this help at http://mandrivausers.org/lofiversion/index.php/t50594.html. Phew. At last, I can now use the iPod without Windoze and without Apple software.

managing photos without facebook or flickr

I got tired of the unreliable photo upload of facebook and found the bandwidth and size limitations of flickr too, er, restrictive, so I looked around for something else. I came across Coppermine Gallery and IMHO it is brilliant.
The online manual tells you exactly how to set it up and it worked first time. I am pleased to say it works with FastHosts (my webspace provider). There is a slight deterioation in image quality that you don't get with facebook or flickr. I think this is combination of me making smaller jpgs and the fact that Coppermine is using GD. It can use ImageMagic where available. I am not sure which one is supposed to be the best.
So, all I need to do now is add menu options to my web site to refer to the various albums.

The pain of building subversion on solaris

I have eventually managed to get subversion 1.5.0 built on solaris (opensolaris running on VirtualBox actually). At the time of writing this, the most recent version of subversion is 1.6.0. However, I have a requirement to use an older version of subversion, 1.5.0. This is because subversion, subclipse and svnant need to all cooperate with each other. This means dropping back to 1.5.0. When I tried to build subversion 1.5.0 on solaris I got a load of link time errors to do with relocatable code in libneon.a. I eventually found a blog at http://sreekalyan.blogspot.com/2005/07/installing-subversion-on-solaris.html which gave me a hint on how to solve the problem. First, I found I had to use version 0.28.1 of neon. The subversion configure does not like a more recent version and says neon is not there! By default, libneon does not build shared libraries. You have to configure with --enable-shared=yes, an undocumented option no less! I then deleted /usr/local/lib/libneon.a so that it could not be picked up by accident. After a configure in subversion I had to hack the value for the neon library, changing it from libneon.la to libneon.so. Wow, what a pain this was!

DSpace, chemical structures, CML and jmol

I have started to put some chemical structures into my DSpace instance. They are going in as CML files. CML is Chemical Markup Language. There is an open source tool called jmol which allows structures to be viewed as 3D rotating images, given a CML file. JMol includes a servlet so that web pages can display these images. I would like to see this used by DSpace. But in the meantime I have set things up so that CML files invoke an external jmol viewer. This is a bit like putting up PDFs and getting the external acrobat reader to display them. Here's how I did it:

• Add a mimetype for XML to the list of registered types. Make the type known (as opposed to unknown or unsupported), and the mimetype chemical/x-cml.
• Download the jmol package from sourceforge and ensure that the script jmol.sh (or jmol.bat on Windoze) has execute permission. On Windoze the environment variable JMOL_HOME must also be defined. On Unix just add the jmol directory to your PATH.
• Test jmol by running the standalone viewer on a CML file. When that works you should be ready.
• Add a CML item to a collection in your Dspace. That's it. Clicking on it will now run the viewer!

It would be great if the 3D image could be in the web page directly, like PDFs can with the browser add-on. But AFAIK there is no such add-on. There is the servlet but this would involve codes changes to DSpace.

Customizing DSpace v1.5.1

Prior to version 1.5.1 of DSpace, customization was done using a separate project called Manakin. The name persists within DSpace, including DSpace documentation, but actually it is all integrated now and customization is done in the dspace tree, not some separate project.

Details on how to customize dspace are very thin on the ground and most talk about how to do it when it was the separate Manakin project. I have managed to find something that works for me. Here's how I did it:

• Stop tomcat.
• Delete the tomcat dir webapps/xmlui.
• go to the dir in which you unpacked dspace. My dir is called dspace-1.5.1-src-release.
• Go to the sub-dir where the themes are stored. The documentation I found leads you to the wrong place. I found I had to go to dspace-xmlui/dspace-xmlui-webapp/src/main/webapp/themes.
• Copy the dir that is closest to the theme you want. Copy the whole dir to a new target theme name. The one I copy is Reference.
• This next step is CRUCIAL - edit sitemap.xmap to make it refer to the new theme name. If you don't then it will still refer to Reference! You need to go to the map:components section near the start. There you will see a section that looks like this:

  <map:component-configurations>
      <global-variables>
          <theme-path>Reference</theme-path>
          <theme-name>put your theme description 
              here</theme-name>
      </global-variables>
  </map:component-configurations>
    

  Change Reference and update the comment.
• Edit dspace/config/xmlui.xconf. Go to the end where you will see the path defined for the default theme. It is Reference/. Note the trailing slash, it is important. Change Reference for your theme name.
• Change something in your theme dir so that the change will be visually obvious. For example you can change the style sheet to refer to a different background image.
• Rebuild dspace with these theme changes. Use the command 'mvn package'. This builds to [dspace-src]/dspace/target.
• Update the dspace installation (which is in c:\dspace for me). Use the command 'ant update'.
• copy the dir dspace/webapps/xmlui to the tomcat webapps dir.
• Restart tomcat.

importing into DSpace

I finally managed to import a text file into DSpace today. It was "Decline of Science in England" by Charles Babbage. Here's how I did it:

• create an import directory. I called mine test-import.
• Create a directory below the import directory. I named it decline, after the book.
• Put the text file into the directory 'decline'.
• Create the file dublin_core.xml, in the 'decline' directory. The file looked like this:

  <dublin_core>
      <dcvalue element="title" qualifier="none">
          Decline of Science in England
      </dcvalue>
  
      <dcvalue element="subject" qualifier="none">
         science
      </dcvalue>
  </dublin_core>
  

• Create a file called content. The file contains a list of filenames, one per line. In this case I had body (which was the name of my text file) and preface, which was a separate preface file I created.

To import the item I then created a community and a collection under it, and gave this command:

bin\dsrun org.dspace.app.itemimport.ItemImport -a -e emailAddress
-m mapfile.out -c 125050010/1469 -s test-import

setting up DSpace and tomcat on windoze

My attention has turned to digital repositories. I looked at Greenstone but had enough problems with even a simple setup (admittedly trying to build from source) that I gave up. So I am now looking at DSpace. I had terrible trouble getting it to work on Windoze with Tomcat. I got it working eventually. Here is the tale of my voyage of discovery.

Prerequisites

Postgres.

goto http://www.postgresql.org/download/ and click on link for windoze. this will take you to a one-click installer for 8.3 the one-click install runs a nice setup wizard. database superuser = postgres,1gandalf. listening port=5432 (default). locale = English, United Kingdom I got the popup "A non-fatal error occured during the cluster initialisation. Please check the installation log in /tmp for details." There did not seem to be a log in either c:\temp or c:\windows\temp. The wizard then went on to completion. The service says it is starting for quite a while then stops. this seems wrong. The windoze event log has a timeout waiting for server startup, preceeded by a fatal error "could not create lock file 'postmaster.pid', permission denied. Went into c:/Program Files/PostgreSQL/8.3 and did a recursive chmod 777. Then restarted the service. this fixed it.

tomcat.

download binary distro for tomcat 5.5 core, windows installer. connector port = 8030 (default is 8080). u,pw=admin,1gandalf service fails to start. turn on debug in tomcat configuration panel, then restart. catalina logfile shows a bind error, address already in use. this was because there was a leftover process that interferred. I found the process using tcpview. need to put tcpview on my web pages. it is much better than netstat. after the kill tomcat restarted just fine.

maven.

it does not seem to come with anything ready for windoze. I unpacked the binary zip and found it is an installation directory. mvn can be run from the bin directory. Add the full pathname of the bin dir to the PATH using the control panel.

postgres (continued)

run PG Admin III (start->PostgreSQL 8.3->pg Admin III. double-click on localhost to connect to the db, enter the password for the postgres user. double-click on loginRoles then rightMouse. Select 'New login role...'. u,pw=dspace,dspace, check 'can create database objects' and 'can create roles'. double-click on databases then rightMouse, select 'new database...'. name=dspace,owner=dspace, UTF8 encoding. privilege properties, add user/group public with connect rights.

dspace.

edit dspace/config/dspace.cfg.
change pathnames so they work for Windoze, e.g /dspace => c:/dspace
change port number to 8030, i.e the one used by tomcat.
db.name = postgres
db.driver = org.postgresql.Driver
db.username = dspace
db.password = dspace
mail.server=mail.company.co.uk
mail.from.address = amarlow@company.com
feedback.recipient = amarlow@company.com
handle.prefix = 123400009
authentication.password.domain.valid = company.com

create c:\dspace cd to where dspace was unpacked. mvn package. this starts by doing lots of downloading and takes a *long* time. it takes over 77 minutes! cd dspace/target/dspace-1.5.1-build.dir. ant fresh_install

using a DOS cmd window:

cd c:\dspace
bin\dsrun org.dspace.administer.CreateAdministrator
email: amarlow@company.com
first name: andrew
last name: marlow
password: 1gandalf

shutdown tomcat. cd to tomcat conf dir edit context.xml putting in the dspace stuff. the context file is new to tomcat v5. restart tomcat. http://localhost:8030/jspui does not work! could not get this to work. tried to copy webapps/jspui to tomcat webapps dir but this also failed, but for a different reason. this gave an error in the tomcat log because it couldn't find ${dspace.dir}\config\dspace.cfg also get a NPE trying to use log4j when not properly configured. problem seems to be to do with the config directory not being copied over. but where to put it?

See http://mailman.mit.edu/pipermail/dspace-general/2008-July/002103.html for someone else who had exactly the same problem as me.

There seems to be a servlet LoadDSpaceConfig that is supposed to manage this and presunably report if there are any problems. But it seems that this is not working. I found this little nuggest in the DSpace manual on page 111, way after the installation instructions!:

The org.dspace.app.webui.servlet.LoadDSpaceConfig servlet is always loaded first. This is a very simple servlet that checks the dspace-config context parameter from the DSpace deployment descriptor, and uses it to locate dspace.cfg. It also loads up the Log4j configuration. It's important that this servlet is loaded first, since if another servlet is loaded up, it will cause the system to try and load DSpace and Log4j configurations, neither of which would be found.

I removed the context stuff from context.xml. This is to pursue a working configuration using the jspui that is copied into the tomcat webapps dir.

I edited webapps/jspui/WEB-INF/web.xml, replacing the dspace.dir param value with the DOS path (C:\dspace.....). This did have an effect. this gave the following error:

log4j:WARN No appenders could be found for logger (org.apache.commons.digester.Digester.sax).
log4j:WARN Please initialize the log4j system properly.
INFO: Loading provided config file: c:\dspace\config\dspace.cfg
INFO: Using dspace provided log configuration (log.init.config)
INFO: Loading: c:/dspace/config/log4j.propertieslog4j:ERROR setFile(null,true) call failed.
java.io.FileNotFoundException: c:\dspace\log\dspace.log (Access is denied)
        at java.io.FileOutputStream.openAppend(Native Method)
        at java.io.FileOutputStream.(Unknown Source)
        at java.io.FileOutputStream.(Unknown Source)
        at org.apache.log4j.FileAppender.setFile(FileAppender.java:289)
        at org.apache.log4j.RollingFileAppender.setFile(RollingFileAppender.java:167)

to fix this I did cd dspace;chmod -R 777 .

this gave

log4j:WARN No appenders could be found for logger (org.apache.commons.digester.Digester.sax).
log4j:WARN Please initialize the log4j system properly.
INFO: Loading provided config file: c:\dspace\config\dspace.cfg
INFO: Using dspace provided log configuration (log.init.config)
INFO: Loading: c:/dspace/config/log4j.properties

this looks alot healthier. Now when I visit http://localhost:8030/jspui/ I get the page I expect. Wow!