From ac870ab80ff695b2735b85ce787aff951721480c Mon Sep 17 00:00:00 2001 From: pvannierop Date: Thu, 27 Jul 2023 16:21:35 +0200 Subject: [PATCH] Update migration docs --- docs/Migration-Guide.md | 39 +++++++++++++++---- .../portal.properties-Reference.md | 2 +- 2 files changed, 32 insertions(+), 9 deletions(-) diff --git a/docs/Migration-Guide.md b/docs/Migration-Guide.md index 7e5ce3197bb..b5177e87276 100644 --- a/docs/Migration-Guide.md +++ b/docs/Migration-Guide.md @@ -1,22 +1,45 @@ # Migration Guide -This page describes various changes deployers will need to make as they deploy newer versions of the portal. + +This page describes various changes deployers will need to make as they deploy newer versions of the portal. - + +## v5.3.17 + +- 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](portal.properties-Reference.md#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](https://github.com/cBioPortal/datahub-study-curation-tools/tree/master/fusion-to-sv-converter) to migrate the fusion files. -- All fusion files on [datahub](https://github.com/cBioPortal/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 -- Study view user setting will be outdated after migration, please follow `Clear Study View User settings` section in [Session Service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](Session-Service-Management.md#Clear-Study-View-User-settings) -- The new default set of transcripts for each gene has changed from `uniprot` to `mskcc`. See the [Mutation Data Annotation Section](./mutation-data-transcript-annotation.md) for more details. To keep the old set of default transcripts add the property `genomenexus.isoform_override_source=uniprot` to [the properties file](https://docs.cbioportal.org/deployment/customization/portal.properties-reference/#properties). + +- All fusion profiles are now required to be migrated to structural variant format. One can use + this [migration tool](https://github.com/cBioPortal/datahub-study-curation-tools/tree/master/fusion-to-sv-converter) + to migrate the fusion files. +- All fusion files on [datahub](https://github.com/cBioPortal/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](Session-Service-Management.md#Clear-Study-View-User-settings) +- The new default set of transcripts for each gene has changed from `uniprot` to `mskcc`. See + the [Mutation Data Annotation Section](./mutation-data-transcript-annotation.md) for more details. To keep the old set + of default transcripts add the property `genomenexus.isoform_override_source=uniprot` + to [the properties file](https://docs.cbioportal.org/deployment/customization/portal.properties-reference/#properties). See the [v5.0.0 release notes](https://github.com/cBioPortal/cbioportal/releases/tag/v5.0.0) 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](https://github.com/cBioPortal/cbioportal/pull/9360)). In theory the migration should be seamless, since the docker container detects an old database version and migrates it automatically. +- Cleans up several old databases ([PR](https://github.com/cBioPortal/cbioportal/pull/9360)). 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](https://github.com/cBioPortal/cbioportal/releases/tag/v4.0.0) 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. + +- 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. + +- 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. diff --git a/docs/deployment/customization/portal.properties-Reference.md b/docs/deployment/customization/portal.properties-Reference.md index 24700086a87..0fbbe48a256 100644 --- a/docs/deployment/customization/portal.properties-Reference.md +++ b/docs/deployment/customization/portal.properties-Reference.md @@ -22,7 +22,7 @@ For example: jdbc:mysql://localhost:3306/cbiodb?zeroDateTimeBehavior=convertToNull&useSSL=false ``` -:warning: The fields `db.host` and `db.portal_db_name` are deprecated. It is recommended to configure the database connection using +:warning: The fields `db.host` and `db.portal_db_name` and `db.use_ssl` are deprecated. It is recommended to configure the database connection using the `db.connection_string` instead. `db.tomcat_resource_name` is required in order to work with the tomcat database connection pool and should have the default value jdbc/cbioportal in order to work correctly with the your WAR file.