[metadb server] Demo clinical integration (import clin sample w/patient imported from igo request)

[ao508]

Prev title: Wrap up data clinical integration message handler for incoming clinical samples

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Dev branch PR: https://github.com/mskcc/cmo-metadb/pull/553/

Dev branch needed to be rebased to the latest master after the changes for handling the CMO patient ID correction went in.

Tests/checks:

resolved (was a typo in mocked patient id i was using)

other thing i ran into:

Patient is now a single node but the DMP alias isn't showing as attached to canonical MetadbPatient node

After updating the patient uuid for the dmp clinical sample being persisted, the DMP alias is linked to the metadb patient but there's an additional cmo alias as well in addition to the original cmo alias that was already attached

Fix:

Had to update the existing patient with any new patient aliases introduced by the clinical sample metadata.

example: existing patient had cmo alias. incoming clinical sample had patient with dmp alias, which now needs to be added to the existing patient node.

[divyamadala30]

Cases tested:

• Persisting a research request/samples 08944_B. Tested this using the endpoint.

• Persisting a clinical sample, file used is attached here

• Persisting a clinical and research sample that use the same patient

Changes made to messageHandlingServiceImpl:

• Commented out the use of crdb service to get patient Id

• Hard coded the patient id to be first C-MP789JR and then changed it C-MP76JR to test case 3. Be careful here, make sure to delete the clinical with the older cmoPatientId before you try to persist it again with the new cmoPatientId.

[ao508]

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