As an IoN DRI researcher, I want to be able to link my de-identified DICOM data with the Epic research study patient.
[x] read in pseudo patient id (particpant_id from dri-to-pixl) in the cli and add to database (pseudo_patient_id in Image table) if has been defined in the csv file (never define it in omop parquet input)
[x] in pixl_dcmd, when getting the Image entity, if it has a pseudo_patient_id then set the DICOM tag to use that, if not then update the database with the generated value from de-identification
Testing
[x] CLI tests
[x] pixl_dcmd tests
IMHO I don't think we need to have this in system tests/integration tests
Documentation
[x] Add to documentation that the pseudo patient ID is persisted to the database, useful for debugging as well as studies which has a pre-defined pseudo ID
Dependencies
No response
Details and Comments
Will need at an alembic migration to add in the new column, default value and be None
Definition of Done / Acceptance Criteria
As an IoN DRI researcher, I want to be able to link my de-identified DICOM data with the Epic research study patient.
particpant_idfromdri-to-pixl) in the cli and add to database (pseudo_patient_idinImagetable) if has been defined in the csv file (never define it in omop parquet input)pixl_dcmd, when getting theImageentity, if it has apseudo_patient_idthen set the DICOM tag to use that, if not then update the database with the generated value from de-identificationTesting
IMHO I don't think we need to have this in system tests/integration tests
Documentation
Dependencies
No response
Details and Comments