Fix inconsistencies in the data organization

[lheisler]

Analysis (and possibly clinical) data is attached to objects using keys, and these keys are used for validation and for downtream decision making.

The way these are set up are inconsistent between data types.

for Mutation data, the key is simply MAF, which is a data type
for Expression data the key is MRNA_EXPRESSION, which is an alteration type (can have three data types, Continuous, discrete, z-score)
for Copy number data the key is a data type (SEG or continuous).

Data types are not unique across alteration types.
The key is better set at Alteration_type:data_type

This will require modifications to the organization of the data, and downstream decision making.

[lheisler]

This took quite a bit of testing to implement, but all seems to be in place. All tests passed at this point, it is possible that there are other parts of the code that need to be accounted for and will keep this in mind with further development. These corrections will allow better extensibility, and implementation of new pipelines.