Set some values automatically when creating items with the batch importers

[Jari Häkkinen]

In the tickets referenced below some smartness was added to the GUI dialogues. I would like to see the same in the batch importers. Currently the batch importer plug-ins require the user to add information to their import files that already is in BASE. I suggest that this is automatically fetched during import.

I have two use cases. Here I use the Array design field for raw bioassay imports.

i) User does not give the array design -> fetch the array design automatically. If no array design exists silently let it be 'none'.

ii) User gives an array design. Check that the given array design does not conflict with the array design implicitly defined through raw bioassay -> scan -> hyb -> slide ... Conflicts should be resolved with error handling options. If correct design was given, silently ignore the field in the file.

The above applies for for the number of arrays in hybridization imports.

Relates to ticket:1104 and ticket:1105.

[Nicklas Nordborg]

i) This assumes that a scan has been given and it should not be any problem to fix this. The array index number can't be assigned automatically because it should be different for different raw bioassays on the same hybridization.

ii) Since we already have this functionality in the "Experiment overview" I think it's not really needed to duplicate that functionality in the importer. What makes this kind of "error" more special than all the other things that the "Experiment overview" also checks? Nothing!

[Jari Häkkinen]

Replying to nicklas:

i) This assumes that a scan has been given and it should not be any problem to fix this. The array index number can't be assigned automatically because it should be different for different raw bioassays on the same hybridization.

No, the index number cannot be set but the total number of arrays in the hybridization can be set during hybridization imports since this is a property of the array design ("Arrays per slide" property). Here of course an array slide must be associated with the hyb.

ii) Since we already have this functionality in the "Experiment overview" I think it's not really needed to duplicate that functionality in the importer. What makes this kind of "error" more special than all the other things that the "Experiment overview" also checks? Nothing!

Nothing special about the error, I just thought that such an error could be detected already during import.

[Nicklas Nordborg]

the total number of arrays in the hybridization can be set during hybridization imports

Oh.. sorry... I did't notice that the subject has changed to importing hybridizations... I'll split this ticket into two new ones, to make things clearer.

[Nicklas Nordborg]

Part i) of this ticket is now replaced by #1264 and #1265.

Part ii) is a "wontfix" since the functionality already exists in the "Item overview".