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Add maintenance
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inodb authored Apr 12, 2023
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# Database Migration
# MSK Maintenance (In Progress)
We provide our cBioPortal's maintenance page publicly in the hope that it may be useful to others

## Database Migration
In the database migration process, we are going to have two main steps: building importers and updating database scheme.

## Building Importers
### Building Importers
- Codebases:
- [cbioportal](https://github.com/cBioPortal/cbioportal)
- [genome nexus annotation pipeline](https://github.com/genome-nexus/genome-nexus-annotation-pipeline)
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- Build all importers at once
- `sh buildproductionjars.sh -sd=true -sgp=true -b=importers`

## Updating Database Scheme
### Updating Database Scheme
Database needs to be updated one by one, we have four main databases: triage, private, genie, and public. Take triage database as an example.
- Migrate one database (e.g. triage)
- SSH into pipeline server
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- Run database migration using script:
- `python3 core/src/main/scripts/migrate_db.py --properties-file src/main/resources/portal.properties --sql db-scripts/src/main/resources/migration.sql`
- Monitor the DB migration process and look for possible errors
- Access database and verify the DB scheme is updated
- Access database and verify the DB scheme is updated

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