Merge pull request #10611 from cBioPortal/custom-driver-config

Customize Custom Driver Name in application.properties file

docs/deployment/customization/Customizing-your-instance-of-cBioPortal.md

@@ -278,19 +278,12 @@ If the download_group is present in user groups then download options are shown
             <td>false</td>
             <td>true / false</td>
         </tr>
-      <tr>
+        <tr>
             <td>google_analytics_profile_id</td>
             <td>enables google analaytics tracking on your site</td>
             <td>disabled</td>
             <td>string</td>
         </tr>
-
-
-
-
-        
-       
-        
    </tbody>
 </table>
 

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

@@ -459,11 +459,13 @@ These data formats are described in the [cBioPortal MAF specifications](/File-Fo
 
 **Enabling custom annotations in the OncoPrint**
 
-To enable functionality for one or both types of custom annotations, enter values for the following properties. These labels will appear in the OncoPrint's "Mutation color" menu.
+To enable functionality for one or both types of custom annotations, enter values for the following properties. These values will appear in the OncoPrint's "Mutation color" menu, Patient View's (mutation, CNA, SV) tables, Results View's mutation table, and Group Comparison View's mutation table.
 
 ```
-oncoprint.custom_driver_annotation.binary.menu_label=Custom driver annotation
-oncoprint.custom_driver_annotation.tiers.menu_label=Custom driver tiers
+oncoprint.custom_driver_annotation.binary.menu_label=Custom Driver
+oncoprint.custom_driver_annotation.binary.menu_description=Custom driver tiers
+oncoprint.custom_driver_annotation.tiers.menu_label=Custom Driver Tiers
+oncoprint.custom_driver_annotation.tiers.menu_description=Custom driver tiers
 ```
 
 **Automatic selection of OncoKB, hotspots and custom annotations**

src/main/java/org/cbioportal/service/FrontendPropertiesServiceImpl.java

@@ -1,14 +1,5 @@
 package org.cbioportal.service;
 
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Paths;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.stream.Collectors;
-
 import jakarta.annotation.PostConstruct;
 import org.cbioportal.service.util.MskWholeSlideViewerTokenGenerator;
 import org.slf4j.Logger;
@@ -19,6 +10,15 @@
 import org.springframework.security.core.context.SecurityContextHolder;
 import org.springframework.stereotype.Service;
 
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.stream.Collectors;
+
 
 // Class adapted from legacy config_service.jsp and GlobalProperties.java
 @Service
@@ -33,6 +33,8 @@ public enum FrontendProperty {
         dat_method("dat.method", null),
         oncoprint_custom_driver_annotation_binary_menu_label(
             "oncoprint.custom_driver_annotation.binary.menu_label", null),
+        oncoprint_custom_driver_annotation_binary_menu_description(
+            "oncoprint.custom_driver_annotation.binary.menu_description", null),
         disabled_tabs("disabled_tabs", null),
         civic_url("civic.url", null),
         oncoprint_custom_driver_annotation_binary_default(
@@ -59,6 +61,8 @@ public enum FrontendProperty {
         show_mdacc_heatmap("show.mdacc.heatmap", null),
         oncoprint_custom_driver_annotation_tiers_menu_label(
             "oncoprint.custom_driver_annotation.tiers.menu_label", null),
+        oncoprint_custom_driver_annotation_tiers_menu_description(
+            "oncoprint.custom_driver_annotation.tiers.menu_description", null),
         patient_view_use_legacy_timeline("patient_view.use_legacy_timeline", null),
         installation_map_url("installation_map_url", null),
         priority_studies("priority_studies", null),

src/main/resources/application.properties.EXAMPLE

@@ -105,6 +105,12 @@ skin.study_view.link_text=To build your own case set, try out our enhanced Study
 # skin.patient_view.copy_number_table.columns.show_on_init=Gene,CNA,Annotation,Cytoband,Cohort
 # skin.patient_view.structural_variant_table.columns.show_on_init=Gene 1,Gene2,Status,Annotation,Variant Class,Event Info,Connection Type
 
+# customizes custom driver and custom driver tiers
+# skin.custom.driver.name=Custom Driver
+# skin.custom.driver.description=Custom driver annotation
+# skin.custom.driver.tiers.name=Custom Driver Tiers
+# skin.custom.driver.tiers.description=Custom driver tiers
+
 # setting controlling the home page
 ## enable this to show studies for which the user does not have permission (will appear greyed out and cannot be analyzed in study view or results view). 
 # skin.home_page.show_unauthorized_studies=false
@@ -252,8 +258,10 @@ ucsc.build=hg19
 oncoprint.defaultview=patient
 
 # OncoPrint driver mutation annotations
-# oncoprint.custom_driver_annotation.binary.menu_label=Custom driver annotation
-# oncoprint.custom_driver_annotation.tiers.menu_label=Custom driver tiers
+# oncoprint.custom_driver_annotation.binary.menu_label=Custom Driver
+# oncoprint.custom_driver_annotation.binary.menu_description=Custom driver annotation
+# oncoprint.custom_driver_annotation.tiers.menu_label=Custom Driver Tiers
+# oncoprint.custom_driver_annotation.tiers.menu_description=Custom driver tiers
 # oncoprint.custom_driver_annotation.binary.default=true
 # oncoprint.custom_driver_annotation.tiers.default=true
 oncoprint.oncokb.default=true