Raw data importer should be able to set annotations on the imported raw bioassay
|Reported by:||Nicklas Nordborg||Owned by:||Nicklas Nordborg|
When importing raw data with the RawDataFileFileImporter it would be very useful if the importer could annotate the raw bioassay at the same time. The annotation types and values to use should be stored with the plug-in configuration. There are two ideas how to implement this:
- Store annotation types and values as regular configuration parameters. This is tricky to implement and involves at least another step in the configuration wizard where annotation types and values must be selected. This solution is not easy to transfer to other plug-ins.
- Make PluginConfiguration implement the Annotatable interface and simply copy annotation values when it is used from the configuration to the raw bioassay when the plug-in is used. This doesn't require any changes to the plug-in configuration and can easily be transfered to all plug-ins that which to use it. The drawback is that annotation types must be marked as usable for plug-in configurations as well as the "real" item type it is intended for. If many plug-ins start to use this feature it could easily lead to overload of annotation types as the plug-in configuration level. Maybe it is possible to extend the plugin api with an interface that can be used to ask the plug-in itself about the item types it can annotate. For example, the raw data importer can only annotation raw bioassays, a sample importer can only annotate samples, etc.
In both cases, the job configuration should include options if the annotations should be applied or not and if existing annotations should be overwritted or not.