From: jandot <jan.aerts@...>
Date: 2008-06-11T23:14:48+09:00
Subject: Re: rake task dependencies: via timestamps table in database

On Jun 9, 9:17 am, Pit Capitain <pit.capit...@gmail.com> wrote:
> 2008/6/6 jandot <jan.ae...@gmail.com>:
>
> > There is some interest in the bioinformatics community for using rake
> > as a workflow tool (...)
> > However, bioinformaticians try to keep their data in databases rather
> > than files. And we found we need some workarounds to get dependencies
> > working. Does anyone know if it would be very difficult to add
> > functionality to rake to check a meta table in a database for
> > timestamps of tasks rather than looking at timestamps of files?
>
> Hi Jan, if you look at the source code of rake's FileTask, you'll see
> that this shouldn't be very difficult. The code consists of only four
> methods and is easy to read. Feel free to ask again if you have more
> questions.
>
> Regards,
> Pit

Thanks for that pointer, Pit. I think I got quite far now based on
FileTask. But something is still wrong. The trouble is that I have no
idea where, so can't really ask specific questions...
It looks like the block passed to a task is not executed.

I've put what I already have on github: http://github.com/jandot/biorake/tree/master

There's a sample directory with an example Rakefile that should work
once the extension is fixed. In addition, there are two test suites
copied from the file tests. Unfortunately, many of the tests still
fail.

If anybody could have a look at the tests and help to get them
running, I would be very thankfull.

Cheers,
jan.