From 036d0a355ca25092699a4571645dac0de58d7ed7 Mon Sep 17 00:00:00 2001
From: ben_orlik <benjamin.orlik2@gmail.com>
Date: Fri, 29 Nov 2024 11:10:12 +0100
Subject: [PATCH] refcator: Deleted .js file and modified datavzrd rule

---
 .../datavzrd/clinical_significance.js         | 23 -------------------
 workflow/rules/datavzrd.smk                   |  1 -
 2 files changed, 24 deletions(-)
 delete mode 100644 workflow/resources/datavzrd/clinical_significance.js

diff --git a/workflow/resources/datavzrd/clinical_significance.js b/workflow/resources/datavzrd/clinical_significance.js
deleted file mode 100644
index ef89e017a..000000000
--- a/workflow/resources/datavzrd/clinical_significance.js
+++ /dev/null
@@ -1,23 +0,0 @@
-function clin_sig(value) {
-  const colorMapping = {
-    "unknown": "#6c757d", // gray
-    "not_provided": "#343a40", // dark gray
-    "other": "#adb5bd", // light gray
-    "benign": "#218838", // green
-    "benign/likely_benign": "#218838", // dark green
-    "likely_benign": "#28a745", // green
-    "protective": "#20c997", // teal
-    "uncertain_significance": "#ffc107", // yellow
-    "conflicting_interpretations_of_pathogenicity": "#17a2b8", // cyan
-    "association": "#007bff", // blue
-    "affects": "#6f42c1", // purple
-    "drug_response": "#6610f2", // dark purple
-    "risk_factor": "#e3342f", // red
-    "likely_pathogenic": "#dc3545", // dark red
-    "pathogenic/likely_pathogenic": "#bd2130", // deep red
-    "pathogenic": "#bd2130" // dark red
-  };
-  
-  const splitValues = value.split(",").map(item => `<span style="color: white; background-color: ${colorMapping[item.trim()]}"class="badge">${item.trim()}</span>`);
-  return splitValues.join(' ');  
-}
diff --git a/workflow/rules/datavzrd.smk b/workflow/rules/datavzrd.smk
index 1c5d6c9c0..d45034a92 100644
--- a/workflow/rules/datavzrd.smk
+++ b/workflow/rules/datavzrd.smk
@@ -68,7 +68,6 @@ rule datavzrd_variants_calls:
         spec_short_observations=workflow.source_path(
             "../resources/datavzrd/spec_short_observations.json"
         ),
-        clin_sig=workflow.source_path("../resources/datavzrd/clinical_significance.js"),
         data_short_observations=workflow.source_path(
             "../resources/datavzrd/data_short_observations.js"
         ),