An Exercise in Irrelevance

Just upgraded to WordPress 2.8. The automatic update didn’t work; this seems to be a continual problem which stems from wordpress not being in the default location. For some reason, it wants to push from the new version rather than pull under these circumstances. Not good.

So, I did the manual upgrade; unfortunately the admin page crashed out with an error:

PHP Fatal error: Call to a member function read() on a non-object in wp-includes/theme.php on line 387

This has been reported here and here

It’s this bit of code causing the problems.

$template_dir = @ dir("$theme_root/$template");
                if ( $template_dir ) {
                        while ( ($file = $template_dir->read()) !== false ) {
// etc

It appeared to be only be my modified version of the theme (Evanesence) causing the problem; it’s not very modified, so I removed them one by one. For no readily apparent reason the problem appears to be a subdirectory called “images.old”. Surely, not a good reason for a crash.

Weird and wonderful.

After a bit of struggle, I now have another literate OWL tool working, along the lines discussed in a previous blog post. Rather than generating the OWL documentation, I now split a Manchester syntax file up, so that I can refer to bits of it. I have this working with OBI, using Protege to produce a single merged ontology file, in Manchester syntax.

The current implementation is rather simple; it produces one file-per-entity in the OWL file which I don’t think is entirely good. When run on OBI, it creates over 1400 files which is a lot. The other problem is that I’ve had to do some dubious hacking to get the file names work out. Firstly, I have to remove spaces and “\”‘s, as wel as “:” which is illegal on NTFS.

There’s also a problem with some of the OWL. Unfortunately, the OBI to OWL conversion process has a reification step which I don’t quite understand the purpose of. This comes out as this sort of anonymous individual. I’m not sure at all how the definition has come out as the rdfs:label, but, for sure, you can’t use this as a filename!

Individual: relationship:genid7

    Annotations:
        rdfs:label "C located_in C' if and only if: given any c that
instantiates C at a time t, there is some c' such that: c' instantiates
C' at time t and c *located_in* c'. (Here *located_in* is the
instance-level location relation.)"@en,
        oboInOwl:hasDbXref relationship:genid8

    Types:
        oboInOwl:Definition

I think I might change the implementation a bit, though. Having 1400 files in one directory is not good. My idea is to serialize the entire file out as latex, with lots of macros, autogenerated.

%% this would appear in the generated file
\newcommand{\OwlClassowlthing}{
  \begin{omn}
Class: owl:Thing
  \end{omn}
}

%% then in your latex file you would do
\owlclass{owl}{Thing}

%% which would just resolve to the class above

The only worry with this is that latex would then have to read a large file into latex, even if most of the macros are not used. This might be really, really slow. Well, we can but try.

As before, the current version is available at git://github.com/phillord/literate_omn.git.