Hi Micha, Micha Bayer writes: > Hi all, > > I am in the final throes of adding the custom interface to the tab2mage > importer plugin but I have one more thing to do before it all works as > specified, and that is to set values for the experimental factors on > each of the raw bioassays added to the experiment so they can all be > displayed in the experiment's detail view (at the moment I am just > getting an empty list). > > I have been looking through the API and the dev docu for this but to no > avail. Can anyone point me in the right direction here? > > I think the raw bioassays should probably be inheriting these values > from the Sample objects they are linked to but I figure out how to a)
yes that is correct. from the GUI you would "edit" the raw bioassay, and go to the inherited annotations tab and select one (usually) of the biosources or samples (whichever is annotated) > add an annotation to a sample or any other item for that matter, and b) > how to let the bioassay inherit this programmatically. in the GUI, I don't think samples/biosources are displayed as inheritable until they actually have some annotations in the GUI go to biosource (or sample) list view and hit the import button. then you can configure/run the annotation importer to add annotations from a tab delimited file using the biosource (or sample) name as the lookup. I can't help very much with the API here because we are mostly using it read-only. However I do happen to know that this code in the migration classes could be useful: http://base.thep.lu.se/browser/branches/2.6-stable/src/clients/migrate/net/sf/basedb/clients/migrate/RawBioAssayTransfer.java#L163 note that there is no sense of channel number in BASE2. I imagine this is going to cause major headaches with tab2mage/MAGE-TAB import/export. I posted a workaround on the list which 'tags' the channel 1 sample on the hybridisation through an inherited annotation. If you can't find it, let me know. It wouldn't work for more than 2 channels of course. hope that helps. cheers, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
