Germline qa (oncokb#1262)

* add gene type badge to variants when searching (oncokb#1240)

* Update protein change in header (oncokb#1245)

* Show genomic indicators associated with variant instead of gene on variant/cancer type pages (oncokb#1247)

* Filter out GIs not associated with variant on variant pages

* Add store changes

* Remove mechanism of inheritence and hide cancer risk cols (oncokb#1251)

* Update clinvar terms (oncokb#1253)

* Support inheritance mechanism in genomic indicators (oncokb#1265)

* Feat/update routes (oncokb#1263)

* update routes to use new gene page

* reroute alteration page and tumor type page

* update screenshot test url

* update mocks

* update server urls

* update remaining urls

* update screenshots

* fix hgvsg response

* fix hgvsg screenshots

* query genome nexus using transcript and not hugo symbol (oncokb#1270)

* query genome nexus using transcript and not hugo symbol

* address comments

* fix screenshot

* Show mutation effect when no pathogenicity (oncokb#1273)

* fix casing for clinical implications for this biomarker tab (oncokb#1272)

* Add gene info table to variant and cancer type pages (oncokb#1274)

* Add gene info

* Update screenshots

* Update table descriptions (oncokb#1275)

* Update gi table (oncokb#1277)

* Remove mechanism of inheritance conversion to allele state (oncokb#1281)

* show coming soon for clinical implications section for germline (oncokb#1280)

* Update germline alteration sorting (oncokb#1283)

* Update store when alteration link changes (oncokb#1284)

* Added v6 news (oncokb#1285)

* Fix altertion page link

* Added TM to oncokb references in the news

* Added Germline Gene Table (oncokb#1287)

* Update news (oncokb#1288)

* Updated news (oncokb#1289)

* Update index.html with new oncokb summary png

* Fix/update news (oncokb#1290)

* fix news for data releast 6.0

* update screenshots

---------

Co-authored-by: Calvin Lu <59149377+calvinlu3@users.noreply.github.com>
Co-authored-by: John Konecny <24961694+jfkonecn@users.noreply.github.com>

Author: 3 people

screenshot-test/AnnotationPages.screenshot.js

@@ -161,7 +161,7 @@ function getMockResponse(url){
       break;
 
     // ROS1
-    case `${SERVER_URL}api/private/utils/numbers/gene/ROS1`:
+    case `${SERVER_URL}api/private/utils/numbers/gene/ROS1?germline=false`:
       res = {
         status: 200,
         contentType: 'application/json',
@@ -175,14 +175,14 @@ function getMockResponse(url){
         body: rose1GeneQuery
       };
       break;
-    case `${SERVER_URL}api/private/search/variants/biological?hugoSymbol=ROS1`:
+    case `${SERVER_URL}api/private/search/variants/biological?hugoSymbol=ROS1&germline=false`:
       res = {
         status: 200,
         contentType: 'application/json',
         body: ros1BiologicalVariants
       };
       break;
-    case `${SERVER_URL}api/private/search/variants/clinical?hugoSymbol=ROS1`:
+    case `${SERVER_URL}api/private/search/variants/clinical?hugoSymbol=ROS1&germline=false`:
       res = {
         status: 200,
         contentType: 'application/json',
@@ -247,7 +247,7 @@ function getMockResponse(url){
       break;
 
     // TP53 Deletion
-    case `${SERVER_URL}api/private/utils/numbers/gene/TP53`:
+    case `${SERVER_URL}api/private/utils/numbers/gene/TP53?germline=false`:
       res = {
         status: 200,
         contentType: 'application/json',
@@ -261,14 +261,14 @@ function getMockResponse(url){
         body: tp53GeneQuery
       };
       break;
-    case `${SERVER_URL}api/private/search/variants/biological?hugoSymbol=TP53`:
+    case `${SERVER_URL}api/private/search/variants/biological?hugoSymbol=TP53&germline=false`:
       res = {
         status: 200,
         contentType: 'application/json',
         body: tp53BiologicalVariants
       };
       break;
-    case `${SERVER_URL}api/private/search/variants/clinical?hugoSymbol=TP53`:
+    case `${SERVER_URL}api/private/search/variants/clinical?hugoSymbol=TP53&germline=false`:
       res = {
         status: 200,
         contentType: 'application/json',
@@ -282,7 +282,7 @@ function getMockResponse(url){
         body: tp53EnsemblGenes
       };
       break;
-    case `${SERVER_URL}api/private/utils/variantAnnotation?hugoSymbol=TP53&referenceGenome=GRCh37&alteration=Deletion`:
+    case `${SERVER_URL}api/private/utils/variantAnnotation?hugoSymbol=TP53&referenceGenome=GRCh37&alteration=Deletion&germline=false`:
       res = {
         status: 200,
         contentType: 'application/json',
@@ -305,7 +305,7 @@ function getMockResponse(url){
       break;
 
     // BRAF V600E
-    case `${SERVER_URL}api/private/utils/numbers/gene/BRAF`:
+    case `${SERVER_URL}api/private/utils/numbers/gene/BRAF?germline=false`:
       res = {
         status: 200,
         contentType: 'application/json',
@@ -319,14 +319,14 @@ function getMockResponse(url){
         body: brafGeneQuery
       };
       break;
-    case `${SERVER_URL}api/private/search/variants/biological?hugoSymbol=BRAF`:
+    case `${SERVER_URL}api/private/search/variants/biological?hugoSymbol=BRAF&germline=false`:
       res = {
         status: 200,
         contentType: 'application/json',
         body: brafBiologicalVariants
       };
       break;
-    case `${SERVER_URL}api/private/search/variants/clinical?hugoSymbol=BRAF`:
+    case `${SERVER_URL}api/private/search/variants/clinical?hugoSymbol=BRAF&germline=false`:
       res = {
         status: 200,
         contentType: 'application/json',
@@ -354,14 +354,14 @@ function getMockResponse(url){
         body: brafV600eRelevantAlterations
       };
       break;
-    case `${SERVER_URL}api/private/utils/variantAnnotation?hugoSymbol=BRAF&referenceGenome=GRCh37&alteration=V600E&tumorType=MEL`:
+    case `${SERVER_URL}api/private/utils/variantAnnotation?hugoSymbol=BRAF&referenceGenome=GRCh37&alteration=V600E&tumorType=MEL&germline=false`:
       res = {
         status: 200,
         contentType: 'application/json',
         body: brafV600eMelanomaVariantAnnotation
       };
       break;
-    case `${SERVER_URL}api/private/utils/variantAnnotation?hugoSymbol=BRAF&referenceGenome=GRCh37&alteration=V600E&tumorType=HCL`:
+    case `${SERVER_URL}api/private/utils/variantAnnotation?hugoSymbol=BRAF&referenceGenome=GRCh37&alteration=V600E&tumorType=HCL&germline=false`:
       res = {
         status: 200,
         contentType: 'application/json',
@@ -441,31 +441,31 @@ describe('Tests with login', () => {
   })
 
   it('Gene Page', async() => {
-    await page.goto(`${CLIENT_URL}gene/ROS1`);
+    await page.goto(`${CLIENT_URL}gene/ROS1/somatic`);
     await page.setViewport(VIEW_PORT_1080);
     await page.waitFor(LONG_WAITING_TIME);
     let image = await page.screenshot(getScreenshotConfig('Gene Page with Login'));
     expect(image).toMatchImageSnapshot({ customSnapshotIdentifier: 'Gene Page with Login' });
   })
 
   it('Alteration Page', async() => {
-    await page.goto(`${CLIENT_URL}gene/TP53/Deletion`);
+    await page.goto(`${CLIENT_URL}gene/TP53/somatic/Deletion`);
     await page.setViewport(VIEW_PORT_1080);
     await page.waitFor(WAITING_TIME);
     let image = await page.screenshot(getScreenshotConfig('Alteration Page with Login'));
     expect(image).toMatchImageSnapshot({ customSnapshotIdentifier: 'Alteration Page with Login' });
   })
 
   it('Alteration Page with Cancer Type - Solid', async() => {
-    await page.goto(`${CLIENT_URL}gene/BRAF/V600E/MEL`);
+    await page.goto(`${CLIENT_URL}gene/BRAF/somatic/V600E/MEL`);
     await page.setViewport(VIEW_PORT_1080);
     await page.waitFor(WAITING_TIME);
     let image = await page.screenshot(getScreenshotConfig('Alteration Page with Cancer Type - Solid with Login'));
     expect(image).toMatchImageSnapshot({ customSnapshotIdentifier: 'Alteration Page with Cancer Type - Solid with Login' });
   })
 
   it('Alteration Page with Cancer Type - Heme', async() => {
-    await page.goto(`${CLIENT_URL}gene/BRAF/V600E/HCL`);
+    await page.goto(`${CLIENT_URL}gene/BRAF/somatic/V600E/HCL`);
     await page.setViewport(VIEW_PORT_1080);
     await page.waitFor(WAITING_TIME);
     let image = await page.screenshot(getScreenshotConfig('Alteration Page with Cancer Type - Heme with Login'));
@@ -525,31 +525,31 @@ describe('Tests without login', () => {
   })
 
   it('Gene Page', async() => {
-    await page.goto(`${CLIENT_URL}gene/ROS1`);
+    await page.goto(`${CLIENT_URL}gene/ROS1/somatic`);
     await page.setViewport(VIEW_PORT_1080);
     await page.waitFor(LONG_WAITING_TIME);
     let image = await page.screenshot(getScreenshotConfig('Gene Page without Login'));
     expect(image).toMatchImageSnapshot({ customSnapshotIdentifier: 'Gene Page without Login' });
   })
 
   it('Alteration Page', async() => {
-    await page.goto(`${CLIENT_URL}gene/TP53/Deletion`);
+    await page.goto(`${CLIENT_URL}gene/TP53/somatic/Deletion`);
     await page.setViewport(VIEW_PORT_1080);
     await page.waitFor(WAITING_TIME);
     let image = await page.screenshot(getScreenshotConfig('Alteration Page without Login'));
     expect(image).toMatchImageSnapshot({ customSnapshotIdentifier: 'Alteration Page without Login' });
   })
 
   it('Alteration Page with Cancer Type - Solid', async() => {
-    await page.goto(`${CLIENT_URL}gene/BRAF/V600E/MEL`);
+    await page.goto(`${CLIENT_URL}gene/BRAF/somatic/V600E/MEL`);
     await page.setViewport(VIEW_PORT_1080);
     await page.waitFor(WAITING_TIME);
     let image = await page.screenshot(getScreenshotConfig('Alteration Page with Cancer Type - Solid without Login'));
     expect(image).toMatchImageSnapshot({ customSnapshotIdentifier: 'Alteration Page with Cancer Type - Solid without Login' });
   })
 
   it('Alteration Page with Cancer Type - Heme', async() => {
-    await page.goto(`${CLIENT_URL}gene/BRAF/V600E/HCL`);
+    await page.goto(`${CLIENT_URL}gene/BRAF/somatic/V600E/HCL`);
     await page.setViewport(VIEW_PORT_1080);
     await page.waitFor(WAITING_TIME);
     let image = await page.screenshot(getScreenshotConfig('Alteration Page with Cancer Type - Heme without Login'));
@@ -600,7 +600,7 @@ describe('Tests on mobile view (< large grid)', () => {
     await page.evaluate(() => {
       localStorage.setItem('oncokb-user-token', 'oncokb-public-demo-admin-token');
     });
-    await page.goto(`${CLIENT_URL}gene/BRAF/V600E/HCL`);
+    await page.goto(`${CLIENT_URL}gene/BRAF/somatic/V600E/HCL`);
     await page.setViewport(MOBILE_VIEW_PORT);
     await page.waitFor(WAITING_TIME);
     let image = await page.screenshot(getScreenshotConfig('Alteration Page with Cancer Type - With login - Mobile'));
@@ -611,7 +611,7 @@ describe('Tests on mobile view (< large grid)', () => {
     await page.evaluate(() => {
       localStorage.removeItem('oncokb-user-token');
     });
-    await page.goto(`${CLIENT_URL}gene/BRAF/V600E/HCL`);
+    await page.goto(`${CLIENT_URL}gene/BRAF/somatic/V600E/HCL`);
     await page.setViewport(MOBILE_VIEW_PORT);
     await page.waitFor(WAITING_TIME);
     let image = await page.screenshot(getScreenshotConfig('Alteration Page with Cancer Type - Without login - Mobile'));