Add initial CDx page #1055

calvinlu3 · 2023-11-15T21:23:55Z

This fixes https://github.com/oncokb/oncokb-pipeline/issues/200

Todo:

Add table sorting
Update logic for CDx cancer type filtering
Update CDx data

calvinlu3 · 2023-11-15T21:24:56Z

Latest updates to CDx page after weekly meeting.

calvinlu3 · 2023-11-20T21:11:44Z

Changes with Search Biomarker replaces with Gene dropdown and alteration search

calvinlu3 · 2023-12-07T00:03:12Z

src/main/webapp/app/pages/companionDiagnosticDevicesPage/companionDiagnosticDevicePage.tsx

+export interface ICompanionDiagnosticDevice {
+  name: string;
+  manufacturer: string;
+  platformType?: string | null;
+  biomarkerAssociation: IBiomarkerAssociation;
+  specimenTypes?: string[];
+}
+
+interface IBiomarkerAssociation {
+  gene: string;
+  alterations: string[];
+  drugs: string[];
+  cancerType: string;
+}


Once we start using the rc branch from transcript, these models should be auto generated.

calvinlu3 · 2023-12-07T00:03:45Z

src/main/webapp/app/shared/utils/FileUtils.ts

+export function downloadFile(
+  fileName: string,
+  content: string,
+  options: BlobPropertyBag = { type: 'text/tsv' }
+) {
+  const blob = new Blob([content], options);
+  const downloadLink = document.createElement('a');
+  downloadLink.href = URL.createObjectURL(blob);
+  downloadLink.download = fileName;
+  downloadLink.click();
+}


Copied from oncokb-transcript

zhx828 · 2023-12-08T16:08:45Z

src/main/webapp/app/pages/companionDiagnosticDevicesPage/companionDiagnosticDevicePage.tsx

+        gene: ba.gene.hugoSymbol,
+        alterations: ba.alterations.map((a: any) => a.name),
+        drugs: ba.drugs.map((d: any) => d.name),
+        cancerType: ba.cancerType.mainType,


We only use the main type?

calvinlu3 · 2024-03-07T23:49:26Z

src/main/webapp/app/shared/links/FdaSubmissionLink.tsx

@@ -0,0 +1,28 @@
+import React from 'react';


This is new since last review

calvinlu3 · 2024-03-07T23:49:49Z

src/main/webapp/app/shared/utils/Utils.tsx

@@ -928,3 +928,12 @@ export const convertObjectArrayToDelimitedString = (
  }


This is new

calvinlu3 · 2024-03-07T23:54:55Z

src/main/webapp/app/config/constants.tsx

@@ -912,3 +913,10 @@ export const DEFAULT_REFERENCE_GENOME = REFERENCE_GENOME.GRCh37;
 export const DEFAULT_FEEDBACK_ANNOTATION: Feedback = {
  type: FeedbackType.ANNOTATION,
 };
+
+export const FDA_SUBMISSION_URL_SUFFIX = {


This is new

calvinlu3 · 2024-03-07T23:55:36Z

src/main/webapp/app/pages/companionDiagnosticDevicesPage/companionDiagnosticDevicePage.tsx

@@ -0,0 +1,633 @@
+import OncoKBTable, {


There are many changes to this file, so needs to be re-reviewed

zhx828

LGTM, only two minor comments.

zhx828 · 2024-03-18T13:37:09Z

src/main/webapp/app/pages/companionDiagnosticDevicesPage/companionDiagnosticDevicePage.tsx

+  const headers = [
+    'Gene',
+    'Alteration(s)',
+    'Cancer Type',


Should this be Cancer Type(s) as well?

zhx828 · 2024-03-18T13:38:33Z

src/main/webapp/app/pages/companionDiagnosticDevicesPage/companionDiagnosticDevicePage.tsx

+
+  useEffect(() => {
+    const filterPresent =
+      !!relevantCancerTypeSearchKeyword ||


The purpose of adding double exclamation mark seems redundant

Its to convert the value to a boolean. Otherwise if the search keyword was "example", then filterPresent = 'example'

bprize15 · 2024-04-30T19:53:30Z

src/main/webapp/app/pages/newsPage/NewsPageContent.tsx

+        Release of the{' '}
+        <Link to={PAGE_ROUTE.CDX}>
+          "FDA Cleared or Approved Companion Diagnostic Devices"
+        </Link>


Maybe a nit, but I'd add a space between ... Devices and the open parenthesis

bprize15 · 2024-04-30T19:59:57Z

src/main/webapp/app/shared/dropdown/CancerTypeSelect.tsx

+    tissue: '',
+    tumorForm: 'LIQUID',
+  },
+];


Why did we make the decision to hardcode the cancer types into the frontend?

Thanks for catch. Thought I removed this before commit. It was purely for testing purposes.

bprize15 · 2024-04-30T20:00:51Z

src/main/webapp/content/files/companionDiagnosticDevices/companion_diagnostic_devices.json

@@ -0,0 +1,16753 @@
+[


Same question as cancer types

We don't have an API client that connects to oncokb-curation (which is where the CDx data is). We are using a static json file for now.

bprize15

Approved with minor comment. Also just hoping to get some clarification on all the hard coding we're doing here.

calvinlu3 added the do not review label Nov 15, 2023

calvinlu3 force-pushed the cdx-page branch from 56366ad to 1543962 Compare December 6, 2023 23:43

calvinlu3 removed the do not review label Dec 6, 2023

calvinlu3 commented Dec 7, 2023

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calvinlu3 requested a review from zhx828 December 7, 2023 14:38

zhx828 reviewed Dec 8, 2023

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calvinlu3 force-pushed the cdx-page branch from 1f6a334 to 4eac6a9 Compare December 29, 2023 18:50

calvinlu3 force-pushed the cdx-page branch from 4eac6a9 to bcce043 Compare January 22, 2024 23:57

calvinlu3 force-pushed the cdx-page branch from 9399d25 to f07fca8 Compare February 14, 2024 20:30

calvinlu3 commented Mar 7, 2024

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calvinlu3 force-pushed the cdx-page branch 2 times, most recently from 1be4b6e to 312b0ec Compare March 7, 2024 23:54

calvinlu3 commented Mar 7, 2024

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calvinlu3 requested a review from zhx828 March 7, 2024 23:56

zhx828 approved these changes Mar 18, 2024

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calvinlu3 force-pushed the cdx-page branch 2 times, most recently from 21debc5 to 4feabb3 Compare April 10, 2024 14:55

calvinlu3 changed the base branch from master to rc April 29, 2024 15:32

calvinlu3 force-pushed the cdx-page branch 2 times, most recently from 1ac5f25 to ab02493 Compare April 30, 2024 18:18

bprize15 reviewed Apr 30, 2024

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calvinlu3 force-pushed the cdx-page branch from ab02493 to c1bc871 Compare April 30, 2024 20:03

calvinlu3 added 5 commits April 30, 2024 16:15

Add CDx page

5b1433f

Update screenshots

5f8eda3

Update SS

bc29b8b

Make dropdowns multi-selectable

262ae27

Fix CDx news text

f347c83

calvinlu3 force-pushed the cdx-page branch from 3fa8c35 to f347c83 Compare April 30, 2024 20:16

calvinlu3 removed the do not merge label Apr 30, 2024

calvinlu3 merged commit 5153d68 into oncokb:rc Apr 30, 2024
3 checks passed

calvinlu3 deleted the cdx-page branch April 30, 2024 20:18

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Add initial CDx page #1055

Add initial CDx page #1055

calvinlu3 commented Nov 15, 2023 •

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		@@ -928,3 +928,12 @@ export const convertObjectArrayToDelimitedString = (
		}

Add initial CDx page #1055

Add initial CDx page #1055

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