TEMPO-cBio pipeline

[ao508]

1. Add pub/sub topic(s) and permissions for TEMPO-cBio pipeline messages

• SMILE-SERVER:
  • already sub'd to TEMPO events
  • pub: UPDATE_TEMPO_EMBARGO
  • pub: RELEASE_TEMPO_SAMPLES
• CBIO USER:
  • sub: UPDATE_TEMPO_EMBARGO
  • sub: RELEASE_TEMPO_SAMPLES

2. Decide on JSON schema to publish from dashboard to TEMPO-cBio pipeline

• protocol buffers generation

Proposed schema:

- primaryId
- cmoSampleName
- embargoStatus (needs to be resolved from embargo date)
- custodianInformation
- cohortId

Define events that will be handled

3a. publish samples to pipeline (see 2 above for schema)

3b. change in embargo status -> updates/changes attribute for sample in data and is updated next import cycle (process that lives in the smile server that checks periodically)

3c. redacting samples (eventually, low priority)