After OpenPedCan-analysis v12 data release, update API database using the released v12 data with the following steps:
Update OpenPedCan-analysis submodule to v12 release commit.
Add a shell script to download filtered MTP tables for database building.
Adapt database building procedure to use the filtered MTP tables.
Rerun ./db/build_db.sh.
If any assertion fails, handle the failed assertion.
If EFO/ENSG ID changes, update tests/r_test_scripts/test_endpoint_http.R to use the updated EFO/ENSG IDs.
Load updated database to local API database server, with DB_LOCATION=local docker-compose up.
Run tests/run_tests.sh locally.
Push local changes to this repository, so that the local changes with be deployed to remote DEV API server.
Deploy the updated database to DEV server for evaluation.
Create a PR for the changes.
After v12 update PR is approved and merged, the changes will be deployed to QA API HTTP server, and QA API database needs to be updated with v12 database. Then, the updated QA API site needs to be evaluated by FNL team for integration with MTP. After the evaluation, the PRD API HTTP server and database will be updated to transfer v12 tables and plots.
After OpenPedCan-analysis v12 data release, update API database using the released v12 data with the following steps:
./db/build_db.sh.tests/r_test_scripts/test_endpoint_http.Rto use the updated EFO/ENSG IDs.DB_LOCATION=local docker-compose up.tests/run_tests.shlocally.After v12 update PR is approved and merged, the changes will be deployed to QA API HTTP server, and QA API database needs to be updated with v12 database. Then, the updated QA API site needs to be evaluated by FNL team for integration with MTP. After the evaluation, the PRD API HTTP server and database will be updated to transfer v12 tables and plots.