Nicklas Nordborg wrote: > 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? >
done! > 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. > Well, it could be difficult with time before July. I am off work for the whole of June and only one day in a week dedicated to BASE. I will probably start next week, but don't expect anything working before my holidays. I guess this makes it patch for 2.13 rather then 2.12... Pawel > /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 ------------------------------------------------------------------------------ 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
