Nicklas (>), Carl (>>), Nicklas (>>>), Carl (>>>>): > >>> * How do I get the name of a data file contained in a RawBioAssay? > >> You can't with the current web services implementation. It should not be > >> hard to add support for it though. Contributions are welcome. > > > > And gladly given. I'm looking at the ws client/server code now, > > thinking of how to add the functionality. In relation to this, I have > > a few questions/opinions, stemming mainly from my unfamiliarity with > > the data model. > > > > * Why DataFileTypeInfo? Being mainly interested in the data files > > themselves (just as I am interested in projects, experiments and > > assays), I wonder why the queries concern the data file types and not > > the files themselves. There's probably a good reason, but I don't see > > it -- especially if you can only have one file of each type. > > The use case we had to solve was to "download the CEL and CDF files used > in an experiment". To be able to do that you need to know the file > types.
I see. > And since we are now trying to support other platforms than > Affymetrix there may very well be other types of files present in BASE. > That is the reason that you have to use the DataFileTypeInfo item. Ok. Could two different file types be present in the same RawBioAssay? To me it seems that they can, at least theoretically. Will it occur in practice? > > * Having a DataFileInfo would benefit my webservices client in two > > ways: firstly DataFileInfo.getName() would naturally map to a file > > name like "3T315.CEL", whereas the current DataFileTypeInfo.getName() > > maps to "CEL file". The latter is not useful to me. Is it to someone > > else? (Though I agree, of course, that it's the natural choice for a > > "name" property on a file type.) > > I think the type of file is more important than the actual name of the file. In a situation where non-Affymetrix files are used, they might well be. I'm in a situation, however, where I want to download and save the files to disk. I could make up unique names locally, but it strikes me as more intuitive if I just used the names the files already have. > > * Secondly, it would make the API for downloading a file easier. > > Instead of writing something like this with DataFileTypeInfo: > > > > <http://pastebin.com/mdadc5f2> > > > > I could write something like this with the (conjectural) class DataFileInfo: > > > > <http://pastebin.com/mdf451ba> > > But you would not know what kind of file you have downloaded with this code. No, only its extension and its contents, the same as before the file was uploaded. A file type is an extrinsic criterion added along with the file. In a data model where the FileInfo class existed, one could conceive of a *Client method providing a back-link to the file type of a FileInfo. > > Since I suspect that good reasons underlie the choice of > > DataFileTypeInfo in favour of something like DataFileInfo, I'm > > thinking of where best to put the methods I want, and also whether or > > not it would be a good idea to introduce something like DataFileInfo. > > It should be FileInfo, since you should just add "Info" to the core > class name. It might also be useful to also have FileSetMemberInfo. The > FileSetMember may have some information about if the file has been > validated or not. Sounds good. > > I'm still willing to implement the things myself, but design guidance > > would be much appreciated. > > Well, it is hard to give much advice in this case. You'll need an *Info > class to hold the information that is going to be sent with the web > service. The hard part is to decide what properties should go in here. > The general rule is that only "simple" values, like numbers and strings > should be added. > > You may need a *Service class and a *Client class. If we get a FileInfo > class it would certainly be useful to have a FileService class as well. > It should at least have a getById() method and a getFiles() method and a > download() method. You can check the other service classes. Thank you. I will look deeper into this, and see what I can come up with. Since I don't have access to a Base 2 server, I guess the code would have to be reviewed after I submit it. // Carl ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
