Pawel Sztromwasser wrote:
> Hello,
> We have been exporting some experiments lately to ArrayExpress and 
> noticed that protocols need to have their own ArrayExpress IDs. 
> Currently we have to add them manually to export file generated in BASE 
> (Tab2MageExporter), but it would be fairly easy to have it done 
> automatically by the plugin. If there only was a place to store it in 
> BASE2...
> Would it be possible to have it as externalId (like BioMaterials have)? 
> Or maybe it is better to enable annotations for protocols? This way it 
> would be possible to add even more "programaticaly accessible" 
> information to protocols. How do you think: which of these two is easier 
> to implement? And which one makes more sense?

I don't know if one method is better than the other. Biomaterials have both
an externalId and annotations. Maybe there is a need for both. The drawback
with the externalId approach is that it is rather undefined what it should be
used for. Originally it was some kind of idea that it should point to some
external sample/clinical database that could possible store sensitive 
and that BASE can't have access to. I don't know if anyone is using the
externalId at all.

I think both approaches should be rather easy to implement. The hardest
part is probably to update the web interface but since the desired functionality
exists elsewhere there is a lot of code to look at (and to copy and paste).

> If any of these is straight-forward enough, I will probably go for a 
> hack like additional column in Protocols table, using description field 
> or similar, but I don't really like hack solutions. Thus, if you are 
> also interested in implementing such a functionality, I am willing to 
> contribute some code/time.

I don't see any reason not to have the functionality. We will appreciate any
contributions. Since both functions require changes to the database you must
work against the trunk source code and there are a few "bookkeeping" things to
consider, but we can help you with that. Can you create one ticket for the
externalId approach and one ticket for the annotation approach to the BASE 

When you have code to submit it is simple to generate at patch with the command
'ant svn.diff' and upload/attach the generated file to the ticket.

What timeframe do you have on this? We have not set a date for BASE 2.12 yet, 
expect to have most things completed within a few weeks. We are also doing some 
work on plug-ins and extensions that are related so it may be up to a month 
everything is finished.


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