Feature/fix submit to core #439

jfkonecn · 2024-09-17T15:45:58Z

@zhx828 it looks like nothing is submitted when an accept all is done. Is that behavior we want?

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

Handle when Instant json element is a json object

…odal helper (oncokb#432)

The getSession is an async method which updates the loading status.

Avoid fetching management info repeatedly

jfkonecn · 2024-09-17T15:49:07Z

src/main/webapp/app/pages/curation/review/ReviewPage.tsx

@@ -125,7 +121,7 @@ const ReviewPage: React.FunctionComponent<IReviewPageProps> = (props: IReviewPag
        isGermline,
        isAcceptAll: true,
        gene: geneData,
-        entrezGeneId: props.geneEntity.entrezGeneId,
+        entrezGeneId: geneEntity?.entrezGeneId as number,


No longer using the prop entity since it's already fetched within this component.

jfkonecn · 2024-09-17T15:50:28Z

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

+      const protectCurrent = shouldProtect(valuePath, currentPath);
+      const protectParent = shouldProtect(valuePath, parentPath);


Need to protect the whole object if the parent is in the valuePath since we don't want to drop the whole object if another value was added.

…cokb#444)

…#445)

zhx828

Looking good!

zhx828 · 2024-10-02T21:51:05Z

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

+
+/**
+ * Recursively filters the provided object to include only the last reviewed elements
+ * or elements that where just accepted.


Suggested change

* or elements that where just accepted.

* or elements that were just accepted.

* 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 <5400599+zhx828@users.noreply.github.com> Co-authored-by: Hongxin <jackson.zhang.828@gmail.com> Co-authored-by: Calvin Lu <59149377+calvinlu3@users.noreply.github.com> Co-authored-by: oncokb-bot <dev.oncokb@gmail.com> Co-authored-by: bprize15 <148106517+bprize15@users.noreply.github.com> * 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 <5400599+zhx828@users.noreply.github.com> Co-authored-by: Hongxin <jackson.zhang.828@gmail.com> Co-authored-by: Calvin Lu <59149377+calvinlu3@users.noreply.github.com> Co-authored-by: oncokb-bot <dev.oncokb@gmail.com> Co-authored-by: bprize15 <148106517+bprize15@users.noreply.github.com> --------- Co-authored-by: Hongxin <jackson.zhang.828@gmail.com> Co-authored-by: Hongxin <5400599+zhx828@users.noreply.github.com> Co-authored-by: Calvin Lu <59149377+calvinlu3@users.noreply.github.com> Co-authored-by: oncokb-bot <dev.oncokb@gmail.com> Co-authored-by: bprize15 <148106517+bprize15@users.noreply.github.com>

zhx828 and others added 12 commits August 22, 2024 08:56

Handle when Instant json element is a json object

ce5ea2e

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

Merge pull request oncokb#424 from zhx828/hot-fix

c3ce224

Handle when Instant json element is a json object

Textarea in review mode should fit text content (oncokb#427)

462c4c4

Update pom version

565bc5b

Fix reject cancer type name review (oncokb#428)

f661d40

Add reference to oncokb sop alteration nomenclature in add mutation m…

2d1016a

…odal helper (oncokb#432)

Update pom version

d831031

Avoid fetching management info repeatedly

7f64f9b

Do not rerender the side bar when loading session

6575c8c

The getSession is an async method which updates the loading status.

Fix drug code not selectable (oncokb#435)

fee10a2

Merge pull request oncokb#434 from zhx828/fix-user-page

e0d7e91

Avoid fetching management info repeatedly

Bump actions to latest version (oncokb#438)

860dbab

jfkonecn force-pushed the feature/fix-submit-to-core branch from 72343f0 to 49c04b0 Compare September 17, 2024 15:46

jfkonecn commented Sep 17, 2024

View reviewed changes

jfkonecn force-pushed the feature/fix-submit-to-core branch from 49c04b0 to a67f82e Compare September 17, 2024 15:53

jfkonecn requested a review from zhx828 September 17, 2024 15:54

bprize15 and others added 3 commits September 19, 2024 09:45

resize text area when input changes (oncokb#440)

5cc5a79

add sorting by firebase index (oncokb#443)

8f0b194

Delete mutation/tumor/treatment as last step to avoid stale index (on…

f269cf8

…cokb#444)

jfkonecn force-pushed the feature/fix-submit-to-core branch from 27a81a9 to 522a927 Compare September 23, 2024 17:57

jfkonecn added 4 commits September 23, 2024 13:59

Review no longer removes data for core submission

73a11ba

Added comments to useLastReviewOnly

277f1cf

Add children review paths

a449744

Fixed approve all

db4da7b

jfkonecn force-pushed the feature/fix-submit-to-core branch from 522a927 to db4da7b Compare September 23, 2024 17:59

jfkonecn and others added 4 commits September 23, 2024 14:00

Fixed UI tests

f03fd79

Fixed UI tests

67e996c

break in middle of word to fix collapsible title overlfow (oncokb#442)

908422a

Change searchEntities to readHandler instead of updateHandler (oncokb…

79bcf58

…#445)

jfkonecn and others added 11 commits September 25, 2024 07:32

Fixed merge conflicts

452c9ba

Fixed submit all

00878aa

Fixed submission bug

c61d25c

Fixed data validation tool (oncokb#447)

f3e0d76

Allow curating mutation summary (oncokb#433)

0d93628

Fixed merge conflicts

d15bb26

Fixed submit all

7eab67a

Fixed tests

eed47b0

Fixed gene type submissions

9bb39ae

Removed last review check inside getevidences and gene type

908b2f1

Added mutation summary

9cc51f0

zhx828 approved these changes Oct 2, 2024

View reviewed changes

jfkonecn merged commit dafac59 into oncokb:feature/submit-to-core Oct 3, 2024
2 checks passed

jfkonecn deleted the feature/fix-submit-to-core branch October 3, 2024 11:28

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Feature/fix submit to core #439

Feature/fix submit to core #439

jfkonecn commented Sep 17, 2024 •

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jfkonecn Sep 17, 2024

jfkonecn Sep 17, 2024 •

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zhx828 left a comment

zhx828 Oct 2, 2024

		const protectCurrent = shouldProtect(valuePath, currentPath);
		const protectParent = shouldProtect(valuePath, parentPath);

	* or elements that where just accepted.
	* or elements that were just accepted.

Feature/fix submit to core #439

Feature/fix submit to core #439

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jfkonecn commented Sep 17, 2024 •

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