# Migration Guide

This page describes various changes deployers will need to make as they deploy newer versions of the portal.

# v5 -> v6

  • Override Spring Application Properties:
    • The process of overriding properties has been updated for example previously users could do the following java -Xms2g -Xmx4g -Dauthenticate=saml -jar webapp-runner.jar. Now users must pass Spring Application properties after the .jar and replace -Dauthenticate=false with --authenticate=false. For example java -Xms2g -Xmx4g -jar cbioportal/target/cbioportal-exec.jar --spring.config.location=cbioportal/application.properties --authenticate=false
  • portal.properties migration needed:
    • portal.properties has been renamed to application.properties. This is the Spring Boot default name
    • authenticate values of googleplus, social_auth_google and social_auth_microsoft have been replaced by optional_oauth2
      • If you used this property before without authorization (unlikely, only the public cBioPortal instance uses this), add the property always_show_study_group=PUBLIC and confirm that all studies in your database you'd like to be be public have GROUPS values set to PUBLIC
  • Redis HTTP Session
    • To disable redis session (Must be disabled if redis is not setup) spring.autoconfigure.exclude=org.springframework.boot.autoconfigure.data.redis.RedisAutoConfiguration
    • To enable spring.data.redis.host=localhost spring.data.redis.port=6379
  • Security changes:
    • Properties used to configure Security have changed see security.properties.EXAMPLE
    • SAML changes:
      • need to generate new keys (.jks no longer works)
        • if you have an existing client, update saml keys with newly generate keys
      • if you have an existing client, update redirect_uri to be without port 443
      • You can now use a URL here, instead of metadata XML: spring.security.saml2.relyingparty.registration.cbio-saml-idp.assertingparty.metadata-uri

# v5.3 -> v5.4

  • Remove db.host and db.portal_db_name and db.use_ssl properties from the portal.properties file or JVM parameters. Update property db.connection_string to encode the hostname, port, database and other parameters according to Database Settings documentation and pass via portal.properties file or as JVM parameter.

# v4 -> v5

  • All fusion profiles are now required to be migrated to structural variant format. One can use this migration tool to migrate the fusion files.
  • All fusion files on datahub were migrated to the structural variant format and their molecular profile ids were renamed from {study_id}_fusion to {study_id}_structural_variants. If you are using these datahub files one would need to re-import them.
  • Study view user setting will be outdated after migration, please follow Clear Study View User settings section in Session Service Management
  • The new default set of transcripts for each gene has changed from uniprot to mskcc. See the Mutation Data Annotation Section for more details. To keep the old set of default transcripts add the property genomenexus.isoform_override_source=uniprot to the properties file.

See the v5.0.0 release notes for more details.

# v3 -> v4

  • Introduces logback package for logging. If you don't have any custom log4j.properties file, no changes are necessary
  • Cleans up several old databases (PR). In theory the migration should be seamless, since the docker container detects an old database version and migrates it automatically.

See the v4.0.0 release notes for more details.

# v2 -> v3

  • Session service is now required to be set up. You can't run it without session service. The recommended way to run cBioPortal is to use the Docker Compose instructions.

# v1 -> v2

  • Changes cBioPortal to a Single Page App (SPA) written in React, Mobx and bootstrap that uses a REST API. It shouldn't change anything for a deployer.