Add INSTRUMENT_MODEL as a constraint for EBI submission

[josenavas]

@antgonza from your recent email it looks like this column is required, so we should update the documentation and the constants for EBI so the system checks for this column.

[antgonza]

I think the best solution is to add the proper values based on the pre-processing pipeline. We currently support 2 values: Illumina and 454. From list here: ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_5/SRA.common.xsd. What do you think?

[josenavas]

That is confusing, I thought that such information was in the PLATFORM column.
Do you know which is the difference between those 2?

[antgonza]

You need both values. See how we add platform and then hardcode the INSTRUMENT_MODEL. However, we should be adding, if LS454 = type454Model. I guess the idea of hardcoding it is that if we add platform you can "guess" the instrument model.

[josenavas]

Makes sense - we should probably grab EBI nomenclature and just create a dictionary that given the PLATFORM we set up the instrument_model if it is not provided in the prep template (if a user provides it - we just provide such information).
Sounds good?

[antgonza]

That's the dream ...

[ackermag]

I will send list
On Oct 1, 2015 8:58 AM, "Antonio Gonzalez" notifications@github.com wrote:

That's the dream ...

—
Reply to this email directly or view it on GitHub
#1483 (comment).

[antgonza]

@ackermag Thanks but I think this is it:
LS454 = com:type454Model ( * )
ILLUMINA = com:typeIlluminaModel ( * )
HELICOS = com:typeHelicosModel
ABI_SOLID = com:typeAbiSolidModel
COMPLETE_GENOMICS = com:typeCGModel
OXFORD_NANOPORE = com:typeOxfordNanoporeModel
PACBIO_SMRT = com:typePacBioModel
ION_TORRENT = com:typeIontorrentModel
CAPILLARY = com:typeCapillaryModel

( * ) We support -- Note that 'UNKNOWN' is supported by Qiita but not is not in EBI's list, what about deleting it?

[ackermag]

That is the list of PLATFORMS not instrument models which is as follows:

Controlled vocabulary for LS454 INSTRUMENT_MODEL:

454 GS

454 GS 20454 GS FLX

454 GS FLX+

454 GS FLX Titanium

454 GS Junior

unspecified

[ackermag]

I am also concerned about this platform:
LS454 (for Roche 454 sequencing - we currently specify platform as FLX or
Titanium to process. Then when I send to EBI I manually change to LS454 or
the submission fails.
DO we need to implement a code change

On Thu, Oct 1, 2015 at 10:20 AM, Gail Ackermann gail.ackermann50@gmail.com
wrote:

That is the list of PLATFORMS not instrument models which is as follows:

Controlled vocabulary for LS454 INSTRUMENT_MODEL:

454 GS

454 GS 20454 GS FLX

454 GS FLX+

454 GS FLX Titanium

454 GS Junior

unspecified

[antgonza]

@ackermag, thanks! This means that we either add this to the required field to the templates or we continue sending unspecified ... and yes that will require some code changes.

[antgonza]

Closed by #1484