Story #18127

Import patient data from Redcap

Added by Peter Amstutz 7 days ago. Updated 6 days ago.

Status:
New
Priority:
Normal
Assigned To:
Category:
-
Target version:
Start date:
Due date:
% Done:

0%

Estimated time:
Story points:
-
Release relationship:
Auto

Description

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.
redcap_snapshot.csv (17.1 KB) redcap_snapshot.csv Peter Amstutz, 09/14/2021 03:32 PM

History

#1 Updated by Peter Amstutz 7 days ago

  • Status changed from New to In Progress

#2 Updated by Peter Amstutz 7 days ago

  • Status changed from In Progress to New
  • Subject changed from Import from Redcap to Import patient data from Redcap
  • Tracker changed from Bug to Story

#3 Updated by Peter Amstutz 7 days ago

#4 Updated by Peter Amstutz 7 days ago

  • Description updated (diff)

#5 Updated by Peter Amstutz 7 days ago

  • Target version set to 2021-09-29 sprint

#6 Updated by Peter Amstutz 6 days ago

  • Assigned To set to Peter Amstutz

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