ctmrbio / claritylims

Customizations for our GenoLogics BaseSpace Clarity LIMS

MIT License

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covid-19: Add biobank export step #166

Open boulund opened 4 years ago

boulund commented 4 years ago

This step needs to link:

Reference code (barcode)
Biobank plate
Biobank plate position
Biobank tube ID

boulund commented 4 years ago

Got the following example from KI Biobank

Samplebarcode;Sampletype;Collectiondate;Region;ResearchSample;Mothersamplebarcode;PNR
*****;******;2020-05-02T13:49:25;Stockholm;Yes;L*******;

We have discussed including something like the following information:

Sample type ("Svalg")
Sampling date (the ServiceRequest creation date from Direkttest)
Region
Barcode for original sample (reference code)
QR code for each biobank tube
Biobank plate ID

boulund commented 4 years ago

I got the account details to the KI Biobank SFTP server where we will upload the data.

boulund commented 4 years ago

I think we have everything we need to start working in this issue now @chichackles. Let's make a plan for how this will be implemented and tested!

boulund commented 4 years ago

We also need to read the biobank consent from direkttest, there is an API endpoint available for grabbing that. I'm fairly sure the KNM API client does not support it at the moment, so we might have to add that to the client as well, since this API endpoint was not present when the KNM API client was created.

196

boulund commented 4 years ago

Drafted some code to do this this weekend in branch cov-166-add-biobank-export

https://github.com/ctmrbio/claritylims/blob/cov-166-add-biobank-export/clarity-ext-scripts/clarity_ext_scripts/covid/export_to_ki_biobank.py