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 information 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 website? 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, but expect to have most things completed within a few weeks. We are also doing some more work on plug-ins and extensions that are related so it may be up to a month before everything is finished. /Nicklas ------------------------------------------------------------------------------ The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com _______________________________________________ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
