cBioPortal · alisman · Aug 1, 2023 · Jul 31, 2023
diff --git a/.../breadcrumbs_are_editable_for_mutation_count_chart_element_chrome_1600x1000.png b/.../breadcrumbs_are_editable_for_mutation_count_chart_element_chrome_1600x1000.png
diff --git a/...shots/reference/show_binary_vs_mutation_count_plot_element_chrome_1600x1000.png b/...shots/reference/show_binary_vs_mutation_count_plot_element_chrome_1600x1000.png
diff --git a/...creenshots/reference/show_binary_vs_os_status_plot_element_chrome_1600x1000.png b/...creenshots/reference/show_binary_vs_os_status_plot_element_chrome_1600x1000.png
diff --git a/...ots/reference/show_category_vs_mutation_count_plot_element_chrome_1600x1000.png b/...ots/reference/show_category_vs_mutation_count_plot_element_chrome_1600x1000.png
diff --git a/...eenshots/reference/show_category_vs_os_status_plot_element_chrome_1600x1000.png b/...eenshots/reference/show_category_vs_os_status_plot_element_chrome_1600x1000.png
diff --git a/...creenshots/reference/show_mutational_bar_chart_dbs_element_chrome_1600x1000.png b/...creenshots/reference/show_mutational_bar_chart_dbs_element_chrome_1600x1000.png
diff --git a/...al/screenshots/reference/show_mutational_bar_chart_element_chrome_1600x1000.png b/...al/screenshots/reference/show_mutational_bar_chart_element_chrome_1600x1000.png
diff --git a/...screenshots/reference/show_mutational_bar_chart_id_element_chrome_1600x1000.png b/...screenshots/reference/show_mutational_bar_chart_id_element_chrome_1600x1000.png
diff --git a/...creenshots/reference/show_mutational_bar_chart_sbs_element_chrome_1600x1000.png b/...creenshots/reference/show_mutational_bar_chart_sbs_element_chrome_1600x1000.png
diff --git a/...able_for_patient_who_has_significant_id_signatures_element_chrome_1600x1000.png b/...able_for_patient_who_has_significant_id_signatures_element_chrome_1600x1000.png
diff --git a/...ient_who_has_significant_id_significant_signatures_element_chrome_1600x1000.png b/...ient_who_has_significant_id_significant_signatures_element_chrome_1600x1000.png
diff --git a/...ble_for_patient_who_has_significant_sbs_signatures_element_chrome_1600x1000.png b/...ble_for_patient_who_has_significant_sbs_signatures_element_chrome_1600x1000.png
diff --git a/...ent_who_has_significant_sbs_significant_signatures_element_chrome_1600x1000.png b/...ent_who_has_significant_sbs_significant_signatures_element_chrome_1600x1000.png
diff --git a/...ient_who_has_significant_v2_significant_signatures_element_chrome_1600x1000.png b/...ient_who_has_significant_v2_significant_signatures_element_chrome_1600x1000.png
diff --git a/...art_for_patient_who_has_significant_dbs_signatures_element_chrome_1600x1000.png b/...art_for_patient_who_has_significant_dbs_signatures_element_chrome_1600x1000.png
diff --git a/...hart_for_patient_who_has_significant_id_signatures_element_chrome_1600x1000.png b/...hart_for_patient_who_has_significant_id_signatures_element_chrome_1600x1000.png
diff --git a/...ient_who_has_significant_id_significant_signatures_element_chrome_1600x1000.png b/...ient_who_has_significant_id_significant_signatures_element_chrome_1600x1000.png
diff --git a/...art_for_patient_who_has_significant_sbs_signatures_element_chrome_1600x1000.png b/...art_for_patient_who_has_significant_sbs_signatures_element_chrome_1600x1000.png
diff --git a/...ent_who_has_significant_sbs_significant_signatures_element_chrome_1600x1000.png b/...ent_who_has_significant_sbs_significant_signatures_element_chrome_1600x1000.png
diff --git a/...rence/show_the_bar_chart_with_percentage_on_y_axis_element_chrome_1600x1000.png b/...rence/show_the_bar_chart_with_percentage_on_y_axis_element_chrome_1600x1000.png
diff --git a/...tip_for_patient_who_has_significant_dbs_signatures_element_chrome_1600x1000.png b/...tip_for_patient_who_has_significant_dbs_signatures_element_chrome_1600x1000.png
diff --git a/...ltip_for_patient_who_has_significant_id_signatures_element_chrome_1600x1000.png b/...ltip_for_patient_who_has_significant_id_signatures_element_chrome_1600x1000.png
diff --git a/...ient_who_has_significant_id_significant_signatures_element_chrome_1600x1000.png b/...ient_who_has_significant_id_significant_signatures_element_chrome_1600x1000.png
diff --git a/...tip_for_patient_who_has_significant_sbs_signatures_element_chrome_1600x1000.png b/...tip_for_patient_who_has_significant_sbs_signatures_element_chrome_1600x1000.png
diff --git a/...ent_who_has_significant_sbs_significant_signatures_element_chrome_1600x1000.png b/...ent_who_has_significant_sbs_significant_signatures_element_chrome_1600x1000.png
diff --git a/...ient_who_has_significant_v2_significant_signatures_element_chrome_1600x1000.png b/...ient_who_has_significant_v2_significant_signatures_element_chrome_1600x1000.png
diff --git a/...ient_who_has_significant_v3_significant_signatures_element_chrome_1600x1000.png b/...ient_who_has_significant_v3_significant_signatures_element_chrome_1600x1000.png
diff --git a/...eference/shows_binary_and_multiple_category_tracks_element_chrome_1600x1000.png b/...eference/shows_binary_and_multiple_category_tracks_element_chrome_1600x1000.png
diff --git a/...tch_between_samples_to_update_mutational_bar_chart_element_chrome_1600x1000.png b/...tch_between_samples_to_update_mutational_bar_chart_element_chrome_1600x1000.png
diff --git a/end-to-end-test/local/specs/core/oncoprint.screenshot.spec.js b/end-to-end-test/local/specs/core/oncoprint.screenshot.spec.js
@@ -34,21 +34,7 @@ const studyes0_oncoprintTabUrl =
 
 const genericArrayUrl =
     CBIOPORTAL_URL +
-    '/results/oncoprint' +
-    '?genetic_profile_ids_PROFILE_MUTATION_EXTENDED=lgg_ucsf_2014_test_generic_assay_mutations' +
-    '&cancer_study_list=lgg_ucsf_2014_test_generic_assay' +
-    '&Z_SCORE_THRESHOLD=2.0' +
-    '&RPPA_SCORE_THRESHOLD=2.0' +
-    '&data_priority=0' +
-    '&profileFilter=0' +
-    '&case_set_id=lgg_ucsf_2014_test_generic_assay_sequenced' +
-    '&gene_list=IDH1' +
-    '&geneset_list=%20' +
-    '&tab_index=tab_visualize' +
-    '&Action=Submit' +
-    '&show_samples=true' +
-    '&generic_assay_groups=lgg_ucsf_2014_test_generic_assay_mutational_signature_binary_v2%2Cmutational_signature_binary_2%2Cmutational_signature_binary_1%3Blgg_ucsf_2014_test_generic_assay_mutational_signature_category_v2%2Cmutational_signature_category_6%2Cmutational_signature_category_8%2Cmutational_signature_category_9';
-
+    '/results?cancer_study_list=lgg_ucsf_2014_test_generic_assay&tab_index=tab_visualize&case_set_id=lgg_ucsf_2014_test_generic_assay_all&Action=Submit&gene_list=IDH1%250ATP53&generic_assay_groups=lgg_ucsf_2014_test_generic_assay_mutational_signature_binary_SBS%2Cmutational_signature_binary_SBS1%2Cmutational_signature_binary_SBS9%3Blgg_ucsf_2014_test_generic_assay_mutational_signature_category_SBS%2Cmutational_signature_category_SBS1%2Cmutational_signature_category_SBS9';
 const SERVER_CLINICAL_TRACK_CONFIG = [
     {
         stableId: 'SUBTYPE',

diff --git a/end-to-end-test/local/specs/core/patientview.screenshot.spec.js b/end-to-end-test/local/specs/core/patientview.screenshot.spec.js
@@ -5,15 +5,15 @@ var waitForPatientView = require('../../../shared/specUtils')
 var { setDropdownOpen } = require('../../../shared/specUtils');
 var assertScreenShotMatch = require('../../../shared/lib/testUtils')
     .assertScreenShotMatch;
-
+const { getElementByTestHandle } = require('../../../shared/specUtils');
 const CBIOPORTAL_URL = process.env.CBIOPORTAL_URL.replace(/\/$/, '');
 const patientViewUrl =
     CBIOPORTAL_URL + '/patient?studyId=teststudy_genepanels&caseId=patientA';
 const ascnPatientViewUrl =
     CBIOPORTAL_URL + '/patient?studyId=ascn_test_study&caseId=FAKE_P001';
 const genericAssayPatientViewUrl =
     CBIOPORTAL_URL +
-    '/patient/mutationalSignatures?studyId=lgg_ucsf_2014_test_generic_assay&sampleId=P01_Pri';
+    '/patient/mutationalSignatures?studyId=lgg_ucsf_2014_test_generic_assay&caseId=P01';
 
 describe('patient view page', function() {
     describe('mutation table for study with ASCN data', () => {
@@ -94,39 +94,57 @@ describe('patient view page', function() {
             });
         });
 
-        it('show stacked bar chart for patient who has significant v3 significant signatures', () => {
+        it('show stacked bar chart for patient who has significant SBS signatures', () => {
             $('div.patientSamples').waitForDisplayed({ timeout: 20000 });
             var res = browser.checkElement('div.patientSamples');
             assertScreenShotMatch(res);
         });
 
-        it('show tooltip for patient who has significant v3 significant signatures', () => {
+        it('show tooltip for patient who has significant SBS signatures', () => {
             $('div.progress').waitForDisplayed({ timeout: 20000 });
             $('div.progress').moveTo({ xOffset: 0, yOffset: 0 });
             assertScreenShotMatch(browser.checkElement('div.patientViewPage'));
         });
 
-        it('show mutational signatures table for patient who has significant v2 significant signatures', () => {
-            selectMutationalSignaturesVersion2();
+        it('show mutational signatures table for patient who has significant SBS signatures', () => {
             var res = browser.checkElement(
                 'div[data-test="MutationalSignaturesContainer"]'
             );
             assertScreenShotMatch(res);
         });
 
-        it('show stacked bar chart for patient who has significant v2 significant signatures', () => {
-            selectMutationalSignaturesVersion2();
+        it('show stacked bar chart for patient who has significant ID signatures', () => {
+            selectMutationalSignaturesVersionID();
             $('div.patientSamples').waitForDisplayed({ timeout: 20000 });
-
             // bar chart does an animation we have to wait for
             browser.pause(5000);
+            var res = browser.checkElement('div.patientSamples');
+            assertScreenShotMatch(res);
+        });
 
+        it('show tooltip for patient who has significant ID signatures', () => {
+            selectMutationalSignaturesVersionID();
+            $('div.progress').waitForDisplayed({ timeout: 20000 });
+            $('div.progress').moveTo({ xOffset: 0, yOffset: 0 });
+
+            $(
+                'div[data-test="SignificantMutationalSignaturesTooltip"]'
+            ).waitForDisplayed();
+
+            assertScreenShotMatch(browser.checkElement('div.patientViewPage'));
+        });
+
+        it('show stacked bar chart for patient who has significant DBS signatures', () => {
+            selectMutationalSignaturesVersionDBS();
+            $('div.patientSamples').waitForDisplayed({ timeout: 20000 });
+            // bar chart does an animation we have to wait for
+            browser.pause(5000);
             var res = browser.checkElement('div.patientSamples');
             assertScreenShotMatch(res);
         });
 
-        it('show tooltip for patient who has significant v2 significant signatures', () => {
-            selectMutationalSignaturesVersion2();
+        it('show tooltip for patient who has significant DBS signatures', () => {
+            selectMutationalSignaturesVersionDBS();
             $('div.progress').waitForDisplayed({ timeout: 20000 });
             $('div.progress').moveTo({ xOffset: 0, yOffset: 0 });
 
@@ -137,14 +155,50 @@ describe('patient view page', function() {
             assertScreenShotMatch(browser.checkElement('div.patientViewPage'));
         });
 
-        it('show mutational signatures table for patient who has significant v2 significant signatures', () => {
-            selectMutationalSignaturesVersion2();
+        it('show mutational signatures table for patient who has significant ID signatures', () => {
+            selectMutationalSignaturesVersionID();
             var res = browser.checkElement(
                 'div[data-test="MutationalSignaturesContainer"]'
             );
             assertScreenShotMatch(res);
         });
     });
+    describe('test the mutational bar chart', () => {
+        it('show mutational bar chart sbs', () => {
+            var res = browser.checkElement(
+                'div[data-test=MutationalSignaturesContainer]'
+            );
+            assertScreenShotMatch(res);
+        });
+        it('show mutational bar chart id', () => {
+            selectMutationalSignaturesVersionID();
+            var res = browser.checkElement(
+                'div[data-test=MutationalSignaturesContainer]'
+            );
+            assertScreenShotMatch(res);
+        });
+        it('show mutational bar chart dbs', () => {
+            selectMutationalSignaturesVersionDBS();
+            var res = browser.checkElement(
+                'div[data-test=MutationalSignaturesContainer]'
+            );
+            assertScreenShotMatch(res);
+        });
+        it('show the bar chart with percentage on y axis', () => {
+            selectPercentageYAxis();
+            var res = browser.checkElement(
+                'div[data-test=MutationalSignaturesContainer]'
+            );
+            assertScreenShotMatch(res);
+        });
+        it('switch between samples to update mutational bar chart', () => {
+            selectSampleMutationalSignature();
+            var res = browser.checkElement(
+                'div[data-test=MutationalSignaturesContainer]'
+            );
+            assertScreenShotMatch(res);
+        });
+    });
 });
 
 const switchGeneFilter = selectedOption => {
@@ -177,11 +231,32 @@ const doVafPlotScreenshotTest = () => {
     assertScreenShotMatch(res);
 };
 
-const selectMutationalSignaturesVersion2 = () => {
+const selectMutationalSignaturesVersionID = () => {
+    $('div.mutationalSignaturesVersionSelector__indicators').waitForDisplayed({
+        timeout: 10000,
+    });
+    $('div.mutationalSignaturesVersionSelector__indicators').click();
+    $('div=Mutational Signature ID').waitForDisplayed({ timeout: 10000 });
+    $('div=Mutational Signature ID').click();
+};
+
+const selectMutationalSignaturesVersionDBS = () => {
     $('div.mutationalSignaturesVersionSelector__indicators').waitForDisplayed({
         timeout: 10000,
     });
     $('div.mutationalSignaturesVersionSelector__indicators').click();
-    $('div=Mutational Signature V2').waitForDisplayed({ timeout: 10000 });
-    $('div=Mutational Signature V2').click();
+    $('div=Mutational Signature DBS').waitForDisplayed({ timeout: 10000 });
+    $('div=Mutational Signature DBS').click();
+};
+const selectPercentageYAxis = () => {
+    getElementByTestHandle('AxisScaleSwitch%').click();
+};
+
+const selectSampleMutationalSignature = () => {
+    $('div.mutationalSignatureSampleSelector__indicators').waitForDisplayed({
+        timeout: 10000,
+    });
+    $('div.mutationalSignatureSampleSelector__indicators').click();
+    $('div=Sample P01_Rec').waitForDisplayed({ timeout: 10000 });
+    $('div=Sample P01_Rec').click();
 };
diff --git a/...t/local/studies/lgg_ucsf_2014_test_generic_assay/data_mutational_signature_binary_DBS.txt b/...t/local/studies/lgg_ucsf_2014_test_generic_assay/data_mutational_signature_binary_DBS.txt
@@ -0,0 +1,12 @@
+ENTITY_STABLE_ID	NAME	DESCRIPTION	URL	P01_Pri	P01_Rec	P02_Pri	P02_Rec	P04_Pri	P04_Rec1	P04_Rec2	P04_Rec3	P05_Pri	P05_Rec	P06_Pri	P06_Rec	P07_Pri	P07_Rec	P08_Pri	P08_Rec	P09_Pri	P09_Rec	P10_Pri	P10_Rec	P11_Pri	P11_Rec	P12_Pri	P12_Rec	P13_Pri	P13_Rec	P15_Pri	P15_Rec	P16_Pri	P16_Rec	P17_Pri_A	P17_Pri_B	P17_Pri_C	P17_Rec1_A	P17_Rec1_B	P17_Rec1_C	P17_Rec1_D	P18_Pri_A	P18_Pri_B	P18_Pri_C	P18_Pri_D	P18_Rec	P21_Pri	P21_Rec	P24_Pri	P24_Rec1	P24_Rec2	P25_Pri	P25_Rec	P26_Pri_A	P26_Pri_B	P26_Rec1_A	P26_Rec1_B	P27_Pri_A	P27_Pri_B	P27_Rec1_A	P27_Rec1_B	P28_Pri	P28_Rec	P29_Pri	P29_Rec
+mutational_signature_binary_DBS1	DBS1 (UV)	Exposure to ultraviolet light	https://cancer.sanger.ac.uk/signatures/dbs/dbs1	true	true	true	true	true	true	true	true	true	true	true	true	true	true	true	true	true	true	true	false	true	true	true	true	true	true	true	true	true	true	true	true	true	true	true	true	true	false	true	true	false	true	true	true	true	true	false	true	true	true	true	true	true	true	true	true	true	true	true	true	true
+mutational_signature_binary_DBS2	DBS2 (Smoking)	Exposure to tobacco smoking as well as other endogenous and/or exogenous mutagens (e.g.	https://cancer.sanger.ac.uk/signatures/dbs/dbs2	false	false	false	false	false	false	false	false	false	false	false	false	true	false	false	true	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	true	false	true	true	false	false	true	false	false	false	false	false	false	false	false	false	true	false	false	false	false	false	false	false
+mutational_signature_binary_DBS3	DBS3 (POLE)	Polymerase epsilon exonuclease domain mutations	https://cancer.sanger.ac.uk/signatures/dbs/dbs3	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false
+mutational_signature_binary_DBS4	DBS4 (Unknown)	Unknown etiology	https://cancer.sanger.ac.uk/signatures/dbs/dbs4	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false
+mutational_signature_binary_DBS5	DBS5 (Platinum)	Prior chemotherapy treatment with platinum drugs	https://cancer.sanger.ac.uk/signatures/dbs/dbs5	false	false	false	false	false	false	false	false	false	false	false	true	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false
+mutational_signature_binary_DBS6	DBS6 (Unknown)	Unknown etiology	https://cancer.sanger.ac.uk/signatures/dbs/dbs6	false	true	false	false	false	false	true	false	false	true	false	false	false	false	false	false	false	false	false	true	false	true	false	false	true	false	false	false	false	false	false	false	false	false	false	false	false	true	false	true	false	true	false	false	false	false	true	false	false	true	true	true	true	false	false	false	false	false	false	false	false
+mutational_signature_binary_DBS7	DBS7 (MMR)	Defective DNA mismatch repair (MMR)	https://cancer.sanger.ac.uk/signatures/dbs/dbs7	false	true	false	false	false	false	false	false	false	true	false	false	false	false	false	false	false	true	false	true	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	true	false	false	false	false	true	true	true	false	false	false	false	false	false	false	false	false	false	false	false
+mutational_signature_binary_DBS8	DBS8 (Unknown)	Unknown	https://cancer.sanger.ac.uk/signatures/dbs/dbs8	false	false	false	false	false	false	false	false	false	true	false	false	false	false	false	false	false	false	false	false	false	false	true	false	false	false	false	false	false	false	false	false	false	false	true	false	true	false	false	false	false	true	false	true	false	false	true	false	false	false	false	false	false	false	true	false	true	false	false	false	false
+mutational_signature_binary_DBS9	DBS9 (Unknown)	Unknown etiology	https://cancer.sanger.ac.uk/signatures/dbs/dbs9	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false
+mutational_signature_binary_DBS10	DBS10 (MMR)	Defective DNA mismatch repair (MMR)	https://cancer.sanger.ac.uk/signatures/dbs/dbs10	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	true	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	true	false	false	false	false	false	false
+mutational_signature_binary_DBS11	DBS11 (Unknown)	Unknown	https://cancer.sanger.ac.uk/signatures/dbs/dbs11	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false	false