Use reviewed content only (oncokb#430)

* Use reviewed content only

* Ignore if in review added state

* Save Genes now checks if added

* Delete parent node if added field is true

* Fixed build

* don't save undefined

* Addressed PR comments

* Addressed PR comments

src/main/webapp/app/service/firebase/firebase-gene-service.ts

@@ -600,9 +600,11 @@ export class FirebaseGeneService {
     let count = 0;
     for (const [hugoSymbol, gene] of Object.entries(geneLookup)) {
       count++;
+      // eslint-disable-next-line no-console
       console.log(`${count} - Saving ${hugoSymbol}...`);
       const nullableVus: Record<string, Vus> | null = vusLookup[hugoSymbol];
       await this.saveGeneWithData(isGermlineProp, hugoSymbol, drugLookup, gene, nullableVus);
+      // eslint-disable-next-line no-console
       console.log('\tDone Saving.');
     }
   };

src/main/webapp/app/shared/api/manual/drive-annotation-api.ts

@@ -35,8 +35,8 @@ export const DriveAnnotationAxiosParamCreator = function (configuration?: Config
       for (const [key, value] of Object.entries(driveAnnotation)) {
         if (typeof value === 'boolean') {
           bodyFormData.append(key, `${value}`);
-        } else {
-          bodyFormData.append(key, value ?? '');
+        } else if (value !== undefined) {
+          bodyFormData.append(key, value);
         }
       }
       localVarRequestOptions.data = bodyFormData;

src/main/webapp/app/shared/util/core-drive-annotation-submission/core-drive-annotation-submission.ts

@@ -1,42 +1,42 @@
 import _ from 'lodash';
 import { Drug, Gene, Mutation, Review, Treatment, Tumor, Vus, DrugCollection } from '../../model/firebase/firebase.model';
+import { useLastReviewedOnly } from '../core-submission-shared/core-submission-utils';
 
-export function getGeneData(geneData: Gene, onlyReviewedContent: boolean, drugList: DrugCollection): true | Gene {
-  const gene = _.cloneDeep(geneData);
-  processData(gene, ['summary', 'background'], onlyReviewedContent);
-  processData(gene.type, ['tsg', 'ocg'], onlyReviewedContent);
+export function getGeneData(geneData: Gene, drugList: DrugCollection): Gene | undefined {
+  const gene = useLastReviewedOnly(geneData);
+  if (gene === undefined) {
+    return undefined;
+  }
+  processData(gene, ['summary', 'background']);
+  processData(gene.type, ['tsg', 'ocg']);
   const tempMutations: Mutation[] = [];
   for (const mutation of gene.mutations ?? []) {
     const tempTumors: Tumor[] = [];
-    if (shouldExclude(onlyReviewedContent, mutation.name_review)) {
+    if (shouldExclude(mutation.name_review)) {
       tempMutations.push(mutation);
       continue;
     }
-    processData(mutation, ['name'], onlyReviewedContent);
-    processData(mutation.mutation_effect, ['oncogenic', 'effect', 'description'], onlyReviewedContent);
+    processData(mutation, ['name']);
+    processData(mutation.mutation_effect, ['oncogenic', 'effect', 'description']);
     for (const tumor of mutation.tumors ?? []) {
-      if (shouldExclude(onlyReviewedContent, tumor.cancerTypes_review)) {
+      if (shouldExclude(tumor.cancerTypes_review)) {
         tempTumors.push(tumor);
         continue;
       }
       // process tumor cancerTypes
-      processData(tumor, ['summary', 'diagnosticSummary', 'prognosticSummary'], onlyReviewedContent);
-      processData(tumor.diagnostic, ['level', 'description', 'excludedRCTs'], onlyReviewedContent);
-      processData(tumor.prognostic, ['level', 'description', 'excludedRCTs'], onlyReviewedContent);
+      processData(tumor, ['summary', 'diagnosticSummary', 'prognosticSummary']);
+      processData(tumor.diagnostic, ['level', 'description', 'excludedRCTs']);
+      processData(tumor.prognostic, ['level', 'description', 'excludedRCTs']);
       for (const ti of tumor.TIs) {
         type TempTreatment = Omit<Treatment, 'name'> & { name: ReturnType<typeof drugUuidToDrug> | string };
         const tempTreatments: TempTreatment[] = [];
         for (const treatment of ti.treatments ?? []) {
-          if (shouldExclude(onlyReviewedContent, treatment.name_review)) {
+          if (shouldExclude(treatment.name_review)) {
             tempTreatments.push(treatment);
-            return true;
+            return undefined;
           }
           (treatment as TempTreatment).name = drugUuidToDrug(treatment.name, drugList);
-          processData(
-            treatment,
-            ['level', 'propagation', 'propagationLiquid', 'indication', 'description', 'fdaLevel'],
-            onlyReviewedContent,
-          );
+          processData(treatment, ['level', 'propagation', 'propagationLiquid', 'indication', 'description', 'fdaLevel']);
         }
         for (const item of tempTreatments) {
           const index = ti.treatments.indexOf(item as Treatment);
@@ -62,20 +62,18 @@ export function getGeneData(geneData: Gene, onlyReviewedContent: boolean, drugLi
   return gene;
 }
 
-function processData<T, K extends keyof T & string>(data: T | undefined, keys: K[], onlyReviewedContent: boolean) {
+function processData<T, K extends keyof T & string>(data: T | undefined, keys: K[]) {
   if (data !== undefined) {
     for (const key of keys) {
       delete data?.[key + '_comments'];
       const reviewKey = key + '_review';
-      const maybeReview = data?.[reviewKey];
-      if (
-        data !== null &&
-        onlyReviewedContent &&
-        typeof maybeReview === 'object' &&
-        maybeReview !== null &&
-        'lastReviewed' in maybeReview
-      ) {
-        data[key] = maybeReview.lastReviewed;
+      const maybeReview: Review | null | undefined = data?.[reviewKey];
+      if (data !== null && typeof maybeReview === 'object' && maybeReview !== null) {
+        if (maybeReview.added) {
+          delete data[key];
+        } else if ('lastReviewed' in maybeReview) {
+          data[key] = maybeReview.lastReviewed as (T & object)[K];
+        }
       }
     }
   }
@@ -91,12 +89,13 @@ export function getVUSData(vus: Vus[]) {
   return vusDataArray;
 }
 
-function shouldExclude(onlyReviewedContent: boolean, reviewObj: Review | undefined) {
-  return (
-    reviewObj &&
-    ((onlyReviewedContent && reviewObj.added === true && reviewObj.promotedToMutation === true && reviewObj.initialUpdate === true) ||
-      (!onlyReviewedContent && reviewObj.removed === true))
-  );
+function shouldExclude(reviewObj: Review | undefined) {
+  /* initialUpdate is true when it is the first time updating excludedRCTs field.
+   * Normally for string fields, we set lastReviewed: "" to empty string.
+   * The "lastReviewed" for excludedRCTs is empty array, which cannot be stored
+   * into firebase, so we created this initialUpdate field to denote that.
+   * */
+  return reviewObj && (reviewObj.added === true || reviewObj.promotedToMutation === true || reviewObj.initialUpdate === true);
 }
 
 function drugUuidToDrug(key: string | undefined, drugList: DrugCollection): Drug[][] | Record<string, unknown> {
@@ -138,10 +137,13 @@ export function getDriveAnnotations(
   { gene, vus, releaseGene }: { gene: Gene | undefined; vus: Vus[] | undefined; releaseGene: boolean },
 ): DriveAnnotation {
   const params: DriveAnnotation = { gene: undefined, vus: undefined, releaseGene: false };
-  if (gene) {
-    params.gene = JSON.stringify(getGeneData(gene, true, drugList));
+  if (gene !== undefined) {
+    const geneData = getGeneData(gene, drugList);
+    if (geneData !== undefined) {
+      params.gene = JSON.stringify(geneData);
+    }
   }
-  if (vus) {
+  if (vus !== undefined) {
     params.vus = JSON.stringify(getVUSData(vus));
   }
   if (releaseGene) {