PHS Pilot Project

Deployment instructions

1. Create and start (or use existing one) standard interactive cluster, no Photon (Optional). Install pyyaml and colorama libraries from PyPi
2. Create (or use existing one) 2X-Small Serverless warehouse, 1 Min 1 Max, Preview channel (Optional)
3. Workspace -> Home -> Create -> Git folder
4. Git repository URL: https://github.com/ysmx-github/phs_pilot.git -> Create Git Folder
5. Open SQL notebook /Workspace/Users/[email protected]/phs_pilot/src/depl/schema_sql
6. Connect to Serverless
7. Run Cell 1
8. Fill the widgets with the catalog name and target folder name (dbr_ssa_clinical and dbr_ddl_clinical are used in this example)
9. Run all
10. Open the volume: Catalog explorer -> dbr_ssa_clinical -> clinical_raw -> clinical_data_volume
11. Download from the shared folder and unzip data.zip and emr_ddl_clinical.zip. Manually upload folders data and emr_ddl_clinical to the volume
12. Open notebook /Workspace/Users/[email protected]/phs_pilot/src/depl/wf1_create, connect to cluster or Serverless, Run all
13. Open notebook /Workspace/Users/[email protected]/phs_pilot/src/depl/wf2_create, connect to cluster or Serverless, Run all
14. Open notebook /Workspace/Users/[email protected]/phs_pilot/src/depl/wf3_create, connect to cluster or Serverless, Run all
15. Open YAML file /Workspace/Users/[email protected]/phs_pilot/src/wf_common/config.yaml, edit db_catalog and volume parameters as needed
16. Open Workflows
17. Run phs_wf1 workflow, review workflow and results
18. Run phs_wf2 workflow, review workflow and results
19. Run phs_wf3 workflow, review workflow and results
20. Open /Workspace/Users/[email protected]/phs_pilot/src/wf3/wf3_dlt_test.sql
21. Select all
22. Copy
23. Open SQL Editor -> New query
24. Paste
25. Select catalog dbr_ssa_clinical and schema clinical_bronze
26. Run CDC tests on the wf3_dlt pipeline