Merge pull request #120 from molgenis/feat/tree_labels

Use decision tree labels for categories
molgenis · Nov 22, 2024 · d4ccf14 · d4ccf14
2 parents 9456d86 + 4e30270
commit d4ccf14
Show file tree

Hide file tree

Showing 5 changed files with 21 additions and 11 deletions.
diff --git a/src/__tests__/apiClient.test.ts b/src/__tests__/apiClient.test.ts
@@ -205,15 +205,15 @@ test("postProcess - sample tree categories", async () => {
   expect(metadata.format["VIPC_S"].categories).toEqual({
     U1: {
       description: "Usable: probably",
-      label: "U1",
+      label: "probably",
     },
     U2: {
       description: "Usable: maybe",
-      label: "U2",
+      label: "maybe",
     },
     U3: {
       description: "Usable: probably not",
-      label: "U3",
+      label: "probably not",
     },
   });
 });
@@ -224,23 +224,23 @@ test("postProcess - decision tree categories", async () => {
   const csqItem = csqItems.find((item) => item.id === "VIPC");
   expect(csqItem.categories).toEqual({
     B: {
-      label: "B",
+      label: "Benign",
     },
     LB: {
-      label: "LB",
+      label: "Likely Benign",
     },
     LP: {
-      label: "LP",
+      label: "Likely Pathogenic",
     },
     LQ: {
       description: "Low quality variants.",
-      label: "LQ",
+      label: "LowQual",
     },
     P: {
-      label: "P",
+      label: "Pathogenic",
     },
     VUS: {
-      label: "VUS",
+      label: "Unknown Significance",
     },
   });
 });

diff --git a/src/__tests__/decisionTree.json b/src/__tests__/decisionTree.json
@@ -326,27 +326,33 @@
       }
     },
     "exit_lq": {
+      "label": "LowQual",
       "description": "Low quality variants.",
       "type": "LEAF",
       "class": "LQ"
     },
     "exit_b": {
+      "label": "Benign",
       "type": "LEAF",
       "class": "B"
     },
     "exit_lb": {
+      "label": "Likely Benign",
       "type": "LEAF",
       "class": "LB"
     },
     "exit_vus": {
+      "label": "Unknown Significance",
       "type": "LEAF",
       "class": "VUS"
     },
     "exit_lp": {
+      "label": "Likely Pathogenic",
       "type": "LEAF",
       "class": "LP"
     },
     "exit_p": {
+      "label": "Pathogenic",
       "type": "LEAF",
       "class": "P"
     }

diff --git a/src/__tests__/sampleTree.json b/src/__tests__/sampleTree.json
@@ -105,16 +105,19 @@
       }
     },
     "exit_u1": {
+      "label": "probably",
       "description": "Usable: probably",
       "type": "LEAF",
       "class": "U1"
     },
     "exit_u2": {
+      "label": "maybe",
       "description": "Usable: maybe",
       "type": "LEAF",
       "class": "U2"
     },
     "exit_u3": {
+      "label": "probably not",
       "description": "Usable: probably not",
       "type": "LEAF",
       "class": "U3"

diff --git a/src/apiClient.ts b/src/apiClient.ts
@@ -119,7 +119,7 @@ export class ApiClient implements Api {
         .reduce(
           (acc, node) => ({
             ...acc,
-            [node.class]: { label: node.class, description: node.description },
+            [node.class]: { label: node.label, description: node.description },
           }),
           {},
         );
@@ -143,7 +143,7 @@ export class ApiClient implements Api {
           .reduce(
             (acc, node) => ({
               ...acc,
-              [node.class]: { label: node.class, description: node.description },
+              [node.class]: { label: node.label, description: node.description },
             }),
             {},
           );

diff --git a/src/index.ts b/src/index.ts
@@ -236,6 +236,7 @@ export interface LeafNode extends Node {
 
 export interface Node {
   type: Type;
+  label: string;
   description: string;
 }