Arvados

Python script to import biopsy data from CSV file exported from Redcap.

• Create project corresponding to each patient
• Assign patient id (MM_0001)
• Match existing patients by MRN (medical record number)
• Update fields that don't exist in Arvados, leave ones that do (to allow for Arvados-local changes)
• Redcap sample_id corresponds to biopsy, create biopsy project
• When the biopsy is going to be sequenced, will record (through Arvados) the DNA/RNA samples

• When creating the initial study, ability to set patient id prefix, will be stored as a property of the study project, when generating a patient id, use prefix from study to which the patients are being added.