Merge pull request #59 from molgenis/feat/treejson

Add decision tree json to api

src/ApiClient.ts

@@ -36,6 +36,7 @@ interface BinaryData extends BinaryDataNode {
   fastaGz?: BinaryDataNode;
   genesGz?: Buffer;
   bam?: BinaryDataNode;
+  decisionTree?: Buffer;
 }
 
 interface BinaryDataNode {
@@ -97,6 +98,11 @@ export class ApiClient implements Api {
     return Promise.resolve(sampleBam !== undefined ? sampleBam : null);
   }
 
+  getDecisionTree(): Promise<Buffer | null> {
+    const decisionTree = this.reportData.binary.decisionTree;
+    return Promise.resolve(decisionTree ? decisionTree : null);
+  }
+
   private get<T extends Resource>(resource: string, params: Params = {}): Promise<PagedItems<T>> {
     return new Promise((resolve, reject) => {
       if (!this.reportData.data[resource]) {

src/ApiData.ts

@@ -36,6 +36,7 @@ export interface EncodedData extends EncodedDataContainer {
   fastaGz?: EncodedDataContainer;
   genesGz?: string;
   bam?: EncodedDataContainer;
+  decisionTree?: string;
 }
 
 export interface Resource {

src/__tests__/ApiClient.test.ts

@@ -61,7 +61,8 @@ beforeEach(() => {
         )
       },
       genesGz: new Base85().encode(Buffer.from(gzipSync(fs.readFileSync(__dirname + '/example.gff')))),
-      bam: { Patient: new Base85().encode(Buffer.from('dummy bam content', 'utf8')) }
+      bam: { Patient: new Base85().encode(Buffer.from('dummy bam content', 'utf8'))},
+      decisionTree: new Base85().encode(Buffer.from(fs.readFileSync(__dirname + '/tree.json'))),
     }
   };
   api = new ApiClient(reportData);
@@ -721,4 +722,27 @@ test('getBam - undefined', async () => {
   api = new ApiClient(reportData);
   const bam = await api.getBam('Patient');
   expect(bam).toBe(null);
+}
+
+);
+
+test('getDecisionTree', async () => {
+  const decisionTree = await api.getDecisionTree();
+  // null check, because size check differs between local machine and Travis
+  expect(decisionTree).not.toBe(null);
 });
+
+test('getDecisionTree - undefined', async () => {
+  const reportData = {
+    metadata: jest.fn() as unknown as Metadata,
+    data: jest.fn() as unknown as Data,
+    base85: {
+      vcfGz: new Base85().encode(Buffer.from(gzipSync(fs.readFileSync(__dirname + '/trio.vcf'))))
+    }
+  };
+
+  api = new ApiClient(reportData);
+  const decisionTree = await api.getDecisionTree();
+  expect(decisionTree).toBe(null);
+});
+

src/__tests__/tree.json

@@ -0,0 +1,76 @@
+{
+  "rootNode": "filter",
+  "nodes": {
+    "filter": {
+      "type": "BOOL",
+      "description": "All filters passed",
+      "query": {
+        "field": "FILTER",
+        "operator": "==",
+        "value": [
+          "PASS"
+        ]
+      },
+      "outcomeTrue": {
+        "nextNode": "vkgl"
+      },
+      "outcomeFalse": {
+        "nextNode": "exit_f"
+      },
+      "outcomeMissing": {
+        "nextNode": "vkgl"
+      }
+    },
+    "vkgl": {
+      "type": "CATEGORICAL",
+      "description": "VKGL classification",
+      "field": "INFO/VKGL",
+      "outcomeMap": {
+        "P": {
+          "nextNode": "exit_t"
+        },
+        "LP": {
+          "nextNode": "exit_t"
+        },
+        "LB": {
+          "nextNode": "exit_f"
+        },
+        "B": {
+          "nextNode": "exit_f"
+        }
+      },
+      "outcomeMissing": {
+        "nextNode": "capice"
+      },
+      "outcomeDefault": {
+        "nextNode": "capice"
+      }
+    },
+    "capice": {
+      "type": "BOOL",
+      "description": "CAPICE score >= 0.02",
+      "query": {
+        "field": "INFO/CAP",
+        "operator": ">=",
+        "value": 0.02
+      },
+      "outcomeTrue": {
+        "nextNode": "exit_t"
+      },
+      "outcomeFalse": {
+        "nextNode": "exit_f"
+      },
+      "outcomeMissing": {
+        "nextNode": "exit_t"
+      }
+    },
+    "exit_t": {
+      "type": "LEAF",
+      "class": "T"
+    },
+    "exit_f": {
+      "type": "LEAF",
+      "class": "F"
+    }
+  }
+}