support default_sort_column config for mutation, CNA, and SV tables (#…

…10630)

Co-authored-by: Qi-Xuan Lu <qlu@carisls.com>

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

@@ -226,6 +226,15 @@ skin.patient_view.copy_number_table.columns.show_on_init=
 skin.patient_view.structural_variant_table.columns.show_on_init=
 ```
 
+### Default sort columns on Mutation, Copy-Number and Structural Variant Tables
+
+Define the column that are going to sort be default in the Mutation, Copy-Number and Structural Variant Tables on the Patient View and the Mutation Table in the Results View.
+Column name should be exactly the same as shown in tables.
+```
+skin.results_view.tables.default_sort_column=
+skin.patient_view.tables.default_sort_column=
+```
+
 ### Define custom sample type colors
 Define the colors of custom sample types in the patient view using a json object with for each sample type a color:
 ```

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

@@ -1,13 +1,10 @@
 package org.cbioportal.service;
 
 import jakarta.annotation.PostConstruct;
-import org.cbioportal.service.util.MskWholeSlideViewerTokenGenerator;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.env.Environment;
-import org.springframework.security.core.Authentication;
-import org.springframework.security.core.context.SecurityContextHolder;
 import org.springframework.stereotype.Service;
 
 import java.io.BufferedReader;
@@ -177,6 +174,8 @@ public enum FrontendProperty {
         skin_results_view_mutation_table_columns_show_on_init("skin.results_view.mutation_table.columns.show_on_init", null),
         skin_patient_view_copy_number_table_columns_show_on_init("skin.patient_view.copy_number_table.columns.show_on_init", null),
         skin_patient_view_structural_variant_table_columns_show_on_init("skin.patient_view.structural_variant_table.columns.show_on_init", null),
+        skin_results_view_tables_default_sort_column("skin.results_view.tables.default_sort_column", null),
+        skin_patient_view_tables_default_sort_column("skin.patient_view.tables.default_sort_column", null),
         enable_treatment_groups("enable_treatment_groups", null),
         comparison_categorical_na_values("comparison.categorical_na_values", null),
         clinical_attribute_product_limit("clinical_attribute_product_limit", null),

src/main/resources/application.properties.EXAMPLE

@@ -105,11 +105,9 @@ 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
+# controls which column from the mutation tables, CNA tables, and SV tables is used to sort by default
+# skin.results_view.tables.default_sort_column=Annotation
+# skin.patient_view.tables.default_sort_column=Annotation
 
 # 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).