[Gusdev-rad-issues] RAD3 Process Tables deprecation

[Elisabetta M. <man...@pc...>]

Here at CBIL we have decided to deprecate the usage of the tables 
RAD3.Process*** and to utilize instead a new view of 
RAD3.AnalysisResultImp to store the results of a series of 
DataTransformation protocols. The Analysis tables were created 
subsequently to the Process tables and have a more mature layout, which 
should facilitate queries. They were originally created to store 
down-stream analysis results (e.g. for differential expression or 
clustering) but they are also suitable for pre-processing result storage.
The following describes what we are implementing:

1. We have created a RAD3.ProtocolStep table to identify protocols 
consisting of an ordered series of (sub) protocols. Every protocol of the 
latter form is linked through RAD3.ProtocolStep to its components. Its 
type will be "transformation_protocol_series" 
(DataTransformationProtocolType).

2. We'll create a linking table RAD3.StudyAnalysis to facilitate queries.

3. We'll create a new view of RAD3.AnalysisResultImp, called 
RAD3.DataTransformationResult, which will store all results from a series 
of preprocessing steps obtained from protocols with type 
DataTransformationProtocolType. This will be a simple view with just 
5 relevant attributes: table_id, row_id (pointing to the spot or to the 
probeset on the array; a soft link), and 
float_value/int_value/string_value 
(which will be what's now currently stored in RAD3.ProcessResult.value).

4. When a series of processing steps is used, we will only store the 
results from the *final* step and the corresponding protocol will be of 
type "transformation_protocol_series".

5. For processes which are simple normalizations of a given quantification 
(or of a pair of quantifications for 2-channel data), the input to the 
analysis will be a LogicalGroup consisting just of that quantification 
(resp. pair of quantifications). For processes which involve averaging 
across quantifications the input LogicalGroup will contain 2 or more 
quantifications

6. In terms of plugins, the current AnalysisResultLoader in the 
GUS/RAD cvs repository at Sanger will do. 
(Enhancements or auxiliary plugins might be written for the specific case 
in which the analysis is an up-stream (=low level=processing) one. So this 
plugin will do the job that the ProcessResultLoader was doing for the 
Process tables.)

Elisabetta