Use reviewed content only #430

jfkonecn · 2024-08-29T14:37:06Z

I add a function, useLastReviewedOnly, to remove the unreviewed content.

zhx828

Newly created section(new mutation for instance) without approval has been saved using Save Gene button.

zhx828 · 2024-08-29T15:35:06Z

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


zhx828 · 2024-09-05T14:17:05Z

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

-  const gene = _.cloneDeep(geneData);
+  const gene = onlyReviewedContent ? useLastReviewedOnly(geneData, true) : _.cloneDeep(geneData);
+  if (gene === undefined) {
+    return true;


Why we returning boolean here?

because that's what the old code did for error cases, but I'll change that.

zhx828 · 2024-09-05T14:21:22Z

...pp/app/shared/util/core-drive-annotation-submission/core-drive-annotation-submission.spec.ts

@@ -123,6 +123,56 @@ const mockGene = createMockGene({
  }),
  mutations_uuid: '69e454db-db99-4979-a770-482f7937314b',
  mutations: [
+    createMockMutation({


We should also add a test for new cancer type and new treatment.

zhx828 · 2024-09-05T14:22:06Z

src/main/webapp/app/shared/util/core-evidence-submission/core-evidence-submission.spec.ts

@@ -456,6 +459,7 @@ describe('getEvidence to submit to core', () => {
                    prognosticSummary_uuid: 'd9c991e4-1c13-4251-bd5a-fac0344b3470',
                    prognosticSummary: 'Prognostic Summary',
                    prognosticSummary_review: createMockReview({
+                      lastReviewed: 'Prognostic Summary Last Reviewed',


What's the rational for testing Last Reviewed for only prognostic?

I felt like if I tried to test every case it'd get too complicate, but as far as why specifically prognostic summary? There isn't a real reason.

Let's pick few relatively important ones? Could you do oncogenicity/Therapeutic Summary/Tx level

zhx828 · 2024-09-05T14:51:16Z

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

+        if (!isSavingGene) {
+          delete temp.lastReviewed;
+        }


Maybe this is copied over from the legacy, but do you know what this is for?

It doesn't seem like this is needed. It'll remove it. I can't remember why I put it there in the first place.

zhx828 · 2024-09-06T13:40:11Z

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

-      (!onlyReviewedContent && reviewObj.removed === true))
-  );
+function shouldExclude(reviewObj: Review | undefined) {
+  return reviewObj && reviewObj.added === true && reviewObj.promotedToMutation === true && reviewObj.initialUpdate === true;


Based on the comment in firebase.model.ts, added and promotedToMutation can coexist. And look at firebase-gene-service, when promotedToMutation is true, added is always true. Could you take a look?

Yes this appears to be the case. I also couldn't find where intialUpdate is ever true. Does that mean this should exclude logic will always be false?

return reviewObj && (reviewObj.added === true || reviewObj.promotedToMutation === true || reviewObj.initialUpdate === true); based on the conversation, we should update to this.
Could you also update the comment to reflect what Calvin said?

zhx828

Thank you

* 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

* Added core submission logic * Added Save Gene Logic (#385) * Added name changes to review logic (#393) * Added name change to core submission logic * Added missing unit tests * Addessed PR comments * Removed unneeded uuid * added comments to collectUUIDs function * Added gene type submission (#396) * Can now delete evidences (#398) * fixed logging in * fixed build errors * updated drugs mapping * updated drugs mapping * Add releaseGene param when saving gene data to core * Update to allow save all genes * Fix excludedRCTs * Add method to undo gene release * Use reviewed content only (#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 * Feature/fix submit to core (#439) * Handle when Instant json element is a json object The completedDate in the DB could be ISO 8601 string, or json object. I think this has to do with the recent spring boot upgrade, but I can't find the specific version of the change. I will handle both scenarios for now * Textarea in review mode should fit text content (#427) * Update pom version * Fix reject cancer type name review (#428) * Add reference to oncokb sop alteration nomenclature in add mutation modal helper (#432) * Update pom version * Avoid fetching management info repeatedly * Do not rerender the side bar when loading session The getSession is an async method which updates the loading status. * Fix drug code not selectable (#435) * Bump actions to latest version (#438) * resize text area when input changes (#440) * add sorting by firebase index (#443) * Delete mutation/tumor/treatment as last step to avoid stale index (#444) * Review no longer removes data for core submission * Added comments to useLastReviewOnly * Add children review paths * Fixed approve all * Fixed UI tests * Fixed UI tests * break in middle of word to fix collapsible title overlfow (#442) * Change searchEntities to readHandler instead of updateHandler (#445) * Fixed submit all * Fixed submission bug * Fixed data validation tool (#447) * Allow curating mutation summary (#433) * Fixed submit all * Fixed tests * Fixed gene type submissions * Removed last review check inside getevidences and gene type * Added mutation summary --------- Co-authored-by: Hongxin <[email protected]> Co-authored-by: Hongxin <[email protected]> Co-authored-by: Calvin Lu <[email protected]> Co-authored-by: oncokb-bot <[email protected]> Co-authored-by: bprize15 <[email protected]> * Added Vus submissions to core (#456) * Make core API call non-blocking (#454) * Handle when Instant json element is a json object The completedDate in the DB could be ISO 8601 string, or json object. I think this has to do with the recent spring boot upgrade, but I can't find the specific version of the change. I will handle both scenarios for now * Textarea in review mode should fit text content (#427) * Update pom version * Fix reject cancer type name review (#428) * Add reference to oncokb sop alteration nomenclature in add mutation modal helper (#432) * Update pom version * Avoid fetching management info repeatedly * Do not rerender the side bar when loading session The getSession is an async method which updates the loading status. * Fix drug code not selectable (#435) * Bump actions to latest version (#438) * resize text area when input changes (#440) * add sorting by firebase index (#443) * Delete mutation/tumor/treatment as last step to avoid stale index (#444) * break in middle of word to fix collapsible title overlfow (#442) * Change searchEntities to readHandler instead of updateHandler (#445) * Fixed data validation tool (#447) * Allow curating mutation summary (#433) * Parse protein change case insensitive (#441) * Fix adding CDx biomarker association (#450) * use firebase properties directly in backend (#451) * fix references tab (#452) * Added Heap (#448) * Added Heap * Updated CSP * Reduce width so sidebar does not go offscren (#446) * allow comma in mutation name when transcripts present (#453) * allow comma in mutation name when transcripts present * add missing colon * rename transcripts to reference genomes * Make core API call non-blocking * Add tests for stale indices check (#455) * Added loading icon when review is accepted * Update setup-java action * Update pom version * Put feature flag in app config * Now showing loading icon on accept all --------- Co-authored-by: Hongxin <[email protected]> Co-authored-by: Hongxin <[email protected]> Co-authored-by: Calvin Lu <[email protected]> Co-authored-by: oncokb-bot <[email protected]> Co-authored-by: bprize15 <[email protected]> --------- Co-authored-by: Hongxin <[email protected]> Co-authored-by: Hongxin <[email protected]> Co-authored-by: Calvin Lu <[email protected]> Co-authored-by: oncokb-bot <[email protected]> Co-authored-by: bprize15 <[email protected]>

Use reviewed content only

bda4656

jfkonecn requested a review from zhx828 August 29, 2024 14:37

zhx828 requested changes Aug 29, 2024

View reviewed changes

jfkonecn added 2 commits August 30, 2024 08:05

Ignore if in review added state

4f1e315

Save Genes now checks if added

b5585a5

jfkonecn requested a review from zhx828 August 30, 2024 14:38

jfkonecn added 3 commits August 30, 2024 16:49

Delete parent node if added field is true

260028a

Fixed build

d91679c

don't save undefined

7774361

zhx828 requested changes Sep 5, 2024

View reviewed changes

Addressed PR comments

eb4677d

jfkonecn requested a review from zhx828 September 6, 2024 13:05

zhx828 reviewed Sep 6, 2024

View reviewed changes

Addressed PR comments

ba32091

jfkonecn requested a review from zhx828 September 6, 2024 20:56

zhx828 approved these changes Sep 6, 2024

View reviewed changes

jfkonecn merged commit 4204647 into oncokb:feature/submit-to-core Sep 6, 2024
2 checks passed

jfkonecn deleted the submit-to-core-john branch September 6, 2024 21:00

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Use reviewed content only #430

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Use reviewed content only #430

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