Automate WMDA MV4 "homework"

[zabeen]

Homework from MV4 currently involves running specific patient-donor pairs through Atlas and returning the "working out". That means: genotype lists for patient and donor, and the matching genotypes list.

We have debug endpoints that generate this data, but need to automate entire process:

Single new locally running manual testing function that accepts:

• a list of PIDs and DIDs
• location to save the results
• homework set name (will be used to name the result folder)
• match loci

For each PDP:

1. Check if patient is typed at all match loci.
2. Check if donor is typed at A, B, and DRB1.
3. Only if patient and donor are typed at required loci, then continue, else save IDs with missing info to file.
4. Send imputation request for patient to remote Atlas instance
5. Process patient imputation result, and store as a CSV file
6. Repeat 1 & 2 for donor
7. Send matching genotypes request
8. Process matching genotypes result, store as a CSV file
9. Optional (if possible), copy contents of CSV files to a single Excel spreadsheet (existing template is available)

• Results files should be named after the patient/donor/PDP