Update migration docs

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. -
+
+## <v5.3.16 --> 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-- Study view user setting will be outdated after migration, please follow `Clear Study View User settings` section in [Session Service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.

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.