Opened 12 years ago

Closed 10 years ago

Last modified 10 years ago

#1280 closed enhancement (wontfix)

Versioned annotations of reporters

Reported by: Jari Häkkinen Owned by: everyone
Priority: major Milestone:
Component: core Version:
Keywords: Cc:

Description

In BASE today there is only one set of reporter annotations but it would be useful to have versions on reporter annotations. A user should be allowed to select which reporter annotation version/set to use.

A simplistic functional approach would be to require that all reporters are annotated for each new version of annotations. The other, less simple, extreme would be to allow each reporter to keep track of all annotation versions in which the reporter was annotated in. However, I think a normal use case will that reporters are annotated in batch where all reporters on some array design would get new annotations. Maybe the batch would be a specific platform like Illumina, Affymetrix, and similar. I do not believe in a scenario where users themselves are allowed to add annotation version, this work is something that the server administrator must to and monitor.

The reporter table in our production server is large and some queries are fairly slow so I would like to see the above functionality without a negative impact on performance.

I understand that versions on reporter annotations is a large change in the underlying database but this ticket is created to open up a discussion on this subject. So, if you have something to say do so.

Change History (6)

comment:1 Changed 12 years ago by Nicklas Nordborg

This will of course not be able to do without negative impact of performance. A new version of a reporter will add an additional entry into the reporter table which will grow for each new version that is added.

comment:2 in reply to:  1 Changed 12 years ago by Jari Häkkinen

Replying to nicklas:

This will of course not be able to do without negative impact of performance. A new version of a reporter will add an additional entry into the reporter table which will grow for each new version that is added.

Of course, but what if we create a new reporter table for each version? Is that doable? Or maybe we should have a reporter table for each platform/rawdatatype? I think we should really think outside BASE 2 here ... I know it smells like BASE 3. Can we imagine a BASE 3 where we only target this issue? Should we think of a BASE 3? What would the impact on the current plug-ins be if we start playing around with the reporter table? Can the change be made without requiring too much work on the plug-ins?

comment:3 Changed 12 years ago by Nicklas Nordborg

I don't think this ticket requires a BASE 3 no matter what technical solution we decide on. And this will of course affect BASE 2 plug-ins. Instead of starting with the technical side of this, I think it would be better to first capture user requirements. For example, how an admin is supposed to work with reporters, how this would be used in experiments, raw data sets, array designs, plates and other places were reporters are used.

comment:4 Changed 12 years ago by Jari Häkkinen

Milestone: BASE 3.0

comment:5 Changed 10 years ago by Nicklas Nordborg

Resolution: wontfix
Status: newclosed

#1616 implements somewhat similar functionality though it is only possible to clone the current reporter annotations and it is not possible to go back to older versions.

comment:6 Changed 10 years ago by Nicklas Nordborg

Milestone: BASE Future Release
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