Added Clickhouse documentation

dev/clickhouse/DEV_SETUP.md

@@ -8,9 +8,9 @@
 - user: _cbio_ password: _P@ssword1_ with all permissions on the _cbioportal_ database.
 - available on port 3306 on the host system.
 
-3. System with docker and docker compose installed.
+2. System with docker and docker compose installed.
 
-## Setup
+## Clickhouse provisioning
 
 All commands start from the root repository location.
 
@@ -30,3 +30,12 @@ This will start a Clickhouse instance that is available on the host system:
 - username: _cbio_
 - password: _P@ssword1_
 
+## cBioPortal integration with Clickhouse
+
+To connect the Clickhouse database to the cBioportal instance, set the following properties in the portal.properties file:
+
+```
+db.clickhouse.user=cbio
+db.clickhouse.password=P@ssword1
+db.clickhouse.connection_string=jdbc:clickhouse://clickhouse:8123/cbioportal?useSSL=false&allowPublicKeyRetrieval=true&allowLoadLocalInfile=true
+```

docs/deployment/customization/portal.properties-Reference.md

@@ -2,7 +2,7 @@
 
 This page describes the main properties within portal.properties.
 
-## Database Settings
+## MySQL Database Settings
 
 ```
 db.user=
@@ -24,6 +24,22 @@ db.tomcat\_resource\_name is required in order to work with the tomcat database
 db.tomcat_resource_name=jdbc/cbioportal
 ```
 
+## Clickhouse Database Settings
+
+Added connection URL for the clickhouse database introduced during the hackathon
+
+```
+db.clickhouse.user=
+db.clickhouse.password=
+```
+
+Include `db.clickhouse.connection_string` with similar formatting to the standard MySQL connection string.
+
+```
+jdbc:clickhouse://localhost/
+```
+
+
 ## cBioPortal Customization
 
 ### Hide tabs (pages)

src/main/resources/portal.properties.EXAMPLE

@@ -1,7 +1,7 @@
 # app name
 app.name=cbioportal
 
-# database
+# MySQL database
 db.user=cbio_user
 db.password=somepassword
 db.host=localhost:3306
@@ -16,10 +16,10 @@ db.connection_string=jdbc:mysql://localhost:3306/
 #
 # db.tomcat_resource_name=jdbc/cbioportal
 
-# clickhouse configuration
-# db.clickhouse.connection_string=jdbc:ch://clickhouse:8123/cbioportal?user=cbio&zeroDateTimeBehavior=convertToNull&useSSL=false
-# db.clickhouse.user=cbio_user
-# db.clickhouse.password=somepassword
+# clickhouse database
+db.clickhouse.user=cbio_user
+db.clickhouse.password=somepassword
+db.clickhouse.connection_string=jdbc:clickhouse://localhost/
 
 # this should normally be set to false. In some cases you could set this to true (e.g. for testing a feature of a newer release that is not related to the schema change in expected db version above):
 db.suppress_schema_version_mismatch_errors=false