Update database migration documentation

docs/Database-Migration.md

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+# Database Migration
+In the database migration process, we are going to have two main steps: building importers and updating database scheme.
+
+## Building Importers
+- Codebases:
+    - [cbioportal](https://github.com/cBioPortal/cbioportal)
+    - [genome nexus annotation pipeline](https://github.com/genome-nexus/genome-nexus-annotation-pipeline)
+    - [pipelines](https://github.com/knowledgesystems/pipelines)
+- Building single importer:
+    - Take the cbioportal hash and add it to genome nexus annotation pipeline POM -> push to fork
+    - Take the cbioportal hash and new genome nexus annotation pipeline hash (from above) and propagate to pipelines POM; also update db version if db migration is part of change
+    - Login to pipelines server
+    - Sets general env variables needed for building
+        - Run `sh /data/portal-con/scripts/automation-environment.sh`
+    - Specific to cbioportal build, looks for properties and xml files off of $PORTAL_HOME
+        - Run `export PORTAL_HOME=/data/portal-cron/git-repos/cbioportal`
+    - Specify importer to be build
+        - Copy importer properties to `/data/portal-con-git-repos/cbioportal/src/main/resources` (e.g. triage `/data/portal-cron/git-repos/pipelines-configuration/properties/import-triage/*`)
+    - Navigate to pipelines folder
+        - `cd /data/portal-con/git-repos/pipelines`
+    - Build importer
+        - mvn clean install -DskipTests
+- Build multiple importers
+    - Take the cbioportal hash and add it to genome nexus annotation pipeline POM -> push to fork
+    - Take the cbioportal hash and new genome nexus annotation pipeline hash (from above) and propagate to pipelines POM; also update db version if db migration is part of change
+    - Login to pipelines server
+    - Sets general env variables needed for building
+        - Run `sh /data/portal-con/scripts/automation-environment.sh`
+    - Specific to cbioportal build, looks for properties and xml files off of $PORTAL_HOME
+        - Run `export PORTAL_HOME=/data/portal-cron/git-repos/cbioportal`
+    - Go to build importer jars folder
+        - `cd /data/portal-cron/git-repo/pipelines-configuration/build-importer-jars`
+    - (Optional) Remove existing jars
+        - `rm *.jar`
+    - Build all importers at once
+        - `sh buildproductionjars.sh -sd=true -sgp=true -b=importers`
+
+## 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
+    - Checkout to the commit that contains the latest database scheme
+    - Check if property sets up correctly to the right database (triage)
+        - `vi /data/portal-con-git-repos/cbioportal/src/main/resources/portal.properties`
+    - Move to directory
+        - `cd /data/portal-con-git-repos/cbioportal`
+    - 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