Merge pull request #2888 from zhx828/expose-oncokb-api-model

Provide a oncokb model for types are not available through swagger ge…
cBioPortal · Nov 21, 2019 · 79c29c2 · 79c29c2
2 parents 594f846 + fbaf6ba
commit 79c29c2
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Showing 5 changed files with 27 additions and 4 deletions.
diff --git a/commons.webpack.config.js b/commons.webpack.config.js
@@ -7,7 +7,7 @@ var GeneratePackageJsonPlugin =require('generate-package-json-webpack-plugin');
 var TerserPlugin = require('terser-webpack-plugin');
 
 var commit = 'unknown';
-var version = '0.0.23';
+var version = '0.0.24';
 
 const NODE_ENV = process.env.NODE_ENV || 'development';
 
@@ -117,7 +117,7 @@ var config = {
 
     plugins: [
         new webpack.DefinePlugin({
-            'VERSION': version, 
+            'VERSION': version,
             'COMMIT': commit,
             // 'ENV_CBIOPORTAL_URL': isDev && process.env.CBIOPORTAL_URL? JSON.stringify(cleanAndValidateUrl(process.env.CBIOPORTAL_URL)) : '"replace_me_env_cbioportal_url"',
             // 'ENV_GENOME_NEXUS_URL': isDev && process.env.GENOME_NEXUS_URL? JSON.stringify(cleanAndValidateUrl(process.env.GENOME_NEXUS_URL)) : '"replace_me_env_genome_nexus_url"'

diff --git a/src/public-lib/api/model/oncokb.ts b/src/public-lib/api/model/oncokb.ts
@@ -0,0 +1,18 @@
+export enum LevelOfEvidence {
+    LEVEL_0 = "LEVEL_0",
+    LEVEL_1 = "LEVEL_1",
+    LEVEL_2A = "LEVEL_2A",
+    LEVEL_2B = "LEVEL_2B",
+    LEVEL_3A = "LEVEL_3A",
+    LEVEL_3B = "LEVEL_3B",
+    LEVEL_4 = "LEVEL_4",
+    LEVEL_R1 = "LEVEL_R1",
+    LEVEL_R2 = "LEVEL_R2",
+    LEVEL_R3 = "LEVEL_R3",
+    LEVEL_Px1 = "LEVEL_Px1",
+    LEVEL_Px2 = "LEVEL_Px2",
+    LEVEL_Px3 = "LEVEL_Px3",
+    LEVEL_Dx1 = "LEVEL_Dx1",
+    LEVEL_Dx2 = "LEVEL_Dx2",
+    LEVEL_Dx3 = "LEVEL_Dx3",
+}
diff --git a/src/public-lib/index.tsx b/src/public-lib/index.tsx
@@ -39,6 +39,8 @@ export {
     Query
 } from "./api/generated/OncoKbAPI";
 
+export * from './api/model/oncokb';
+
 export {remoteData} from "./api/remoteData";
 
 export * from './lib/ColumnVisibilityResolver';

diff --git a/src/public-lib/lib/OncoKbUtils.ts b/src/public-lib/lib/OncoKbUtils.ts
@@ -1,3 +1,5 @@
+import {LevelOfEvidence} from "../api/model/oncokb";
+
 export const LEVELS = {
     sensitivity: ['4', '3B', '3A', '2B', '2A', '1', '0'],
     resistance: ['R3', 'R2', 'R1'],
@@ -13,7 +15,7 @@ export function generatePartialEvidenceQuery(evidenceTypes?:string)
     return {
         evidenceTypes: evidenceTypes ? evidenceTypes : "GENE_SUMMARY,GENE_BACKGROUND,ONCOGENIC,MUTATION_EFFECT,VUS,MUTATION_SUMMARY,TUMOR_TYPE_SUMMARY,STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY,STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE,INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY,INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE",
         highestLevelOnly: false,
-        levels: ['LEVEL_1', 'LEVEL_2A', 'LEVEL_2B', 'LEVEL_3A', 'LEVEL_3B', 'LEVEL_4', 'LEVEL_R1', 'LEVEL_R2'],
+        levels: [LevelOfEvidence.LEVEL_1, LevelOfEvidence.LEVEL_2A, LevelOfEvidence.LEVEL_2B, LevelOfEvidence.LEVEL_3A, LevelOfEvidence.LEVEL_3B, LevelOfEvidence.LEVEL_4, LevelOfEvidence.LEVEL_R1, LevelOfEvidence.LEVEL_R2],
         source: "cbioportal"
     };
 }

diff --git a/src/shared/lib/OncoKbUtils.ts b/src/shared/lib/OncoKbUtils.ts
@@ -9,6 +9,7 @@ import {
     generatePartialEvidenceQuery,
     LEVELS,
 } from "public-lib/lib/OncoKbUtils";
+import {LevelOfEvidence} from "public-lib/api/model/oncokb";
 
 export function generateIdToIndicatorMap(data:IndicatorQueryResp[]): {[queryId:string]: IndicatorQueryResp}
 {
@@ -120,7 +121,7 @@ export function processEvidence(evidences:EvidenceQueryRes[]) {
                     datum.alteration.push(_datum);
                 } else if (evidence.levelOfEvidence) {
                     //if evidence has level information, that means this is treatment evidence.
-                    if (['LEVEL_0'].indexOf(evidence.levelOfEvidence) === -1) {
+                    if ([LevelOfEvidence.LEVEL_0].indexOf(evidence.levelOfEvidence) === -1) {
                         var _treatment:any = {};
                         _treatment.alterations = evidence.alterations;
                         _treatment.articles = evidence.articles;