From 3f07318cc21296fcf1008424af4acdbe6072a12d Mon Sep 17 00:00:00 2001
From: BasLee <basleenknegt@thehyve.nl>
Date: Thu, 31 Aug 2023 16:49:07 +0200
Subject: [PATCH] Add json prop for custom patient view sample type colors
 (#10336)

---
 .../mskcc/cbio/portal/util/GlobalProperties.java   | 14 ++++++++++++++
 .../customization/portal.properties-Reference.md   | 13 +++++++++++++
 portal/src/main/webapp/config_service.jsp          |  2 ++
 3 files changed, 29 insertions(+)

diff --git a/core/src/main/java/org/mskcc/cbio/portal/util/GlobalProperties.java b/core/src/main/java/org/mskcc/cbio/portal/util/GlobalProperties.java
index 88fbcf4a8ef..18209811460 100644
--- a/core/src/main/java/org/mskcc/cbio/portal/util/GlobalProperties.java
+++ b/core/src/main/java/org/mskcc/cbio/portal/util/GlobalProperties.java
@@ -183,6 +183,12 @@ public void setOncoprintClinicalTracksConfigJson(String property) {
         oncoprintClinicalTracksConfigJson = property; 
     }
 
+    private static String skinPatientViewCustomSampleTypeColorsJson;
+    @Value("${skin.patient_view.custom_sample_type_colors_json:}") // default is empty string
+    public void setSkinPatientViewCustomSampleTypeColorsJson(String property) {
+        skinPatientViewCustomSampleTypeColorsJson = property; 
+    }
+
     // properties for showing the right logo in the header_bar and default logo
     public static final String SKIN_RIGHT_LOGO = "skin.right_logo";
 
@@ -1257,6 +1263,14 @@ public static String getOncoprintClinicalTracksConfigJson() {
         }
     }
     
+    public static String getSkinPatientViewCustomSampleTypeColorsJson() {
+        if (skinPatientViewCustomSampleTypeColorsJson.length() > 0) {
+            return readFile(skinPatientViewCustomSampleTypeColorsJson);
+        } else {
+            return null;
+        }
+    }
+    
     public static String getQuerySetsOfGenes() {
         String fileName = portalProperties.getProperty(SETSOFGENES_LOCATION, null);
         return readFile(fileName);
diff --git a/docs/deployment/customization/portal.properties-Reference.md b/docs/deployment/customization/portal.properties-Reference.md
index 07dc145b1e7..bff32c60fb6 100644
--- a/docs/deployment/customization/portal.properties-Reference.md
+++ b/docs/deployment/customization/portal.properties-Reference.md
@@ -225,6 +225,19 @@ skin.patient_view.copy_number_table.columns.show_on_init=
 skin.patient_view.structural_variant_table.columns.show_on_init=
 ```
 
+### 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:
+```
+skin.patient_view.custom_sample_type_colors_json=classpath:/skin-patient-view-custom-sample-type-colors.json
+```
+Example of json file contents:
+```json
+{
+    "Primary": "green",
+    "Biopsy 3": "#00c040ff"
+}
+```
+
 ### Choose the display name for authenticated users
 
 By default the display name for authenticated users is email, but it can be changed for the user name:
diff --git a/portal/src/main/webapp/config_service.jsp b/portal/src/main/webapp/config_service.jsp
index 1fe5079ae3a..495bce3e1f5 100644
--- a/portal/src/main/webapp/config_service.jsp
+++ b/portal/src/main/webapp/config_service.jsp
@@ -185,6 +185,8 @@
 
         obj.put("oncoprint_clinical_tracks_config_json",GlobalProperties.getOncoprintClinicalTracksConfigJson());
 
+        obj.put("skin_patient_view_custom_sample_type_colors_json", GlobalProperties.getSkinPatientViewCustomSampleTypeColorsJson());
+
         obj.put("authenticationMethod",GlobalProperties.authenticationMethod());
 
         obj.put("mskWholeSlideViewerToken", GlobalProperties.getMskWholeSlideViewerToken());