[MOBY-dev] Problems with Biomoby services in Taverna 1.2

[Tom Oinn]

mark wilkinson wrote:
> We really need to get write-access to the Taverna CVS so that we can
> fix these kinds of things in a timely way... Hint hint :-). Anyone
> from myGrid listening?

What you need to do is TEST YOUR CODE!!! I'll give you access to our CVS 
repository but I'm highly unimpressed that a) noone thought to check 
that the plugin behaviour was equivalent and b) I still have no 
documentation from anyone on the moby team for this code. I know Taverna 
is hardly perfect from a docs standpoint but you can understand my 
reluctance to import code from someone I've never met without any 
evidence of either testing, architecture design, specification or 
documentation.

For the future (i.e. Taverna2) we will reject ALL code (including mine) 
that does not have at least 90% line and branch coverage from unit 
tests, I wish I'd done this first time around but hey, we live and learn 
:) Similarly we will not accept code that is undocumented at both API 
and user level - there is ABSOLUTELY NO POINT in writing some neat 
functionality (such as the object creator) and not producing good 
documentation. Good documentation in this context consists of well 
written English suitable for a user of the workbench along with examples 
and screenshots where appropriate.

In this particular case the behaviour that Rebecca refers to needs to be 
reintroduced, it is imperative that workflows from 1.1 work in 1.2 and 
subsequent versions with no alterations to the workflow - at least no 
manual ones. This might involve adding logic to the parser to transform 
older workflows into the newer form. The main requirement is that moby 
collections be exposed to Taverna's type system, the previous behaviour 
was to split the collections into taverna collections of moby simples 
thus allowing our existing iteration framework to take care of any type 
mismatches. This feature must be reintroduced with some urgency, 
removing it changes the fundamental behaviour of the workflow engine and 
we must avoid doing this.

I am of course largely to blame for not insisting on this prior to the 
release, mea culpa.

Eddie - you have sf.net CVS access to taverna but please tell us via the 
developers mailing list when you change things, don't rely on the cvs 
logs (but do put properly informative messages in them!)

Tom