Core analysis plug-ins need to be aware of bioassaysets that use data in files

[Nicklas Nordborg]

This is related to #1029 and depends on #1050. All existing core plug-ins expect data to be found in the database. When #1050 is in place, they need to be aware of that there are bioassay sets that have data inside files. The plug-ins should not try to load the data from files. Instead their isInContext() method should be implemented in a way that hides the plug-in in those cases. The current core plugins are:

• Base 1 executor
• JEP extra value calculator
• JEP filter
• JEP intensity transformer
• Lowess normalization
• Median ratio normalization
• BioAssaySet exporter