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Merge pull request #10480 from cBioPortal/fix-typos
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Fix path typos in MSK-Maintenance.md
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inodb authored Dec 4, 2023
2 parents 5eea5ec + c5e5e35 commit 9986615
Showing 1 changed file with 6 additions and 6 deletions.
12 changes: 6 additions & 6 deletions docs/MSK-Maintenance.md
Original file line number Diff line number Diff line change
Expand Up @@ -14,22 +14,22 @@ In the database migration process, we are going to have two main steps: building
- 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`
- Run `sh /data/portal-cron/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`
- Make sure the local cbioportal codebase is on the correct git hash at `/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/*`)
- Copy importer properties to `/data/portal-cron/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`
- `cd /data/portal-cron/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`
- Run `sh /data/portal-cron/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`
- Make sure the local cbioportal codebase is on the correct git hash at `/data/portal-cron/git-repos/cbioportal`
Expand Down Expand Up @@ -61,9 +61,9 @@ Database needs to be updated one by one, we have four main databases: triage, pr
- 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`
- `vi /data/portal-cron/git-repos/cbioportal/src/main/resources/portal.properties`
- Move to directory
- `cd /data/portal-con-git-repos/cbioportal`
- `cd /data/portal-cron/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
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