Merge pull request #2838 from adamabeshouse/global-settings2

Global settings menu for results view page
cBioPortal · Nov 21, 2019 · c621f31 · c621f31
2 parents 79c29c2 + d6d98fa
commit c621f31
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Showing 37 changed files with 979 additions and 526 deletions.
diff --git a/.../remote/screenshots/reference/no_session_plots_tab_element_chrome_1600x1000.png b/.../remote/screenshots/reference/no_session_plots_tab_element_chrome_1600x1000.png
diff --git a/.../reference/plots_tab_clinical_vs_molecular_boxplot_element_chrome_1600x1000.png b/.../reference/plots_tab_clinical_vs_molecular_boxplot_element_chrome_1600x1000.png
diff --git a/...eenshots/reference/plots_tab_clinical_vs_molecular_element_chrome_1600x1000.png b/...eenshots/reference/plots_tab_clinical_vs_molecular_element_chrome_1600x1000.png
diff --git a/...e/screenshots/reference/plots_tab_copy_number_view_element_chrome_1600x1000.png b/...e/screenshots/reference/plots_tab_copy_number_view_element_chrome_1600x1000.png
diff --git a/...mote/screenshots/reference/plots_tab_log_scale_off_element_chrome_1600x1000.png b/...mote/screenshots/reference/plots_tab_log_scale_off_element_chrome_1600x1000.png
diff --git a/...molecular_vs_clinical_boxplot,_mutation_search_off_element_chrome_1600x1000.png b/...molecular_vs_clinical_boxplot,_mutation_search_off_element_chrome_1600x1000.png
diff --git a/...ar_vs_molecular_different_genes_different_profiles_element_chrome_1600x1000.png b/...ar_vs_molecular_different_genes_different_profiles_element_chrome_1600x1000.png
diff --git a/...e/plots_tab_molecular_vs_molecular_different_genes_element_chrome_1600x1000.png b/...e/plots_tab_molecular_vs_molecular_different_genes_element_chrome_1600x1000.png
diff --git a/..._tab_molecular_vs_molecular_same_gene_changed_gene_element_chrome_1600x1000.png b/..._tab_molecular_vs_molecular_same_gene_changed_gene_element_chrome_1600x1000.png
diff --git a/...ference/plots_tab_molecular_vs_molecular_same_gene_element_chrome_1600x1000.png b/...ference/plots_tab_molecular_vs_molecular_same_gene_element_chrome_1600x1000.png
diff --git a/...ence/plots_tab_molecular_vs_molecular_swapped_axes_element_chrome_1600x1000.png b/...ence/plots_tab_molecular_vs_molecular_swapped_axes_element_chrome_1600x1000.png
diff --git a/...screenshots/reference/plots_tab_mutation_type_view_element_chrome_1600x1000.png b/...screenshots/reference/plots_tab_mutation_type_view_element_chrome_1600x1000.png
diff --git a/...erence/plots_tab_mutations_profile_with_duplicates_element_chrome_1600x1000.png b/...erence/plots_tab_mutations_profile_with_duplicates_element_chrome_1600x1000.png
diff --git a/.../reference/plots_tab_mutations_vs_clinical_boxplot_element_chrome_1600x1000.png b/.../reference/plots_tab_mutations_vs_clinical_boxplot_element_chrome_1600x1000.png
diff --git a/...s_tab_mutations_wild_type_mode_vs_clinical_boxplot_element_chrome_1600x1000.png b/...s_tab_mutations_wild_type_mode_vs_clinical_boxplot_element_chrome_1600x1000.png
diff --git a/...ts/reference/plots_tab_search_case_id_and_mutation_element_chrome_1600x1000.png b/...ts/reference/plots_tab_search_case_id_and_mutation_element_chrome_1600x1000.png
diff --git a/...ote/screenshots/reference/plots_tab_search_case_id_element_chrome_1600x1000.png b/...ote/screenshots/reference/plots_tab_search_case_id_element_chrome_1600x1000.png
diff --git a/...te/screenshots/reference/plots_tab_search_mutation_element_chrome_1600x1000.png b/...te/screenshots/reference/plots_tab_search_mutation_element_chrome_1600x1000.png
diff --git a/...est/remote/screenshots/reference/session_plots_tab_element_chrome_1600x1000.png b/...est/remote/screenshots/reference/session_plots_tab_element_chrome_1600x1000.png
diff --git a/end-to-end-test/remote/specs/core/mutationsTab.spec.js b/end-to-end-test/remote/specs/core/mutationsTab.spec.js
@@ -1,6 +1,6 @@
 var assert = require('assert');
 var waitForOncoprint = require('../../../shared/specUtils').waitForOncoprint;
-var setOncoprintMutationsMenuOpen = require('../../../shared/specUtils').setOncoprintMutationsMenuOpen;
+var setResultsPageSettingsMenuOpen = require('../../../shared/specUtils').setResultsPageSettingsMenuOpen;
 var goToUrlAndSetLocalStorage = require('../../../shared/specUtils').goToUrlAndSetLocalStorage;
 
 const CBIOPORTAL_URL = process.env.CBIOPORTAL_URL.replace(/\/$/, "");
@@ -9,11 +9,25 @@ describe("mutations tab", function() {
     it("uses VUS filtering", function() {
         goToUrlAndSetLocalStorage(`${CBIOPORTAL_URL}/results/oncoprint?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=acc_tcga_pan_can_atlas_2018&case_set_id=acc_tcga_pan_can_atlas_2018_cnaseq&data_priority=0&gene_list=HSD17B4&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=acc_tcga_pan_can_atlas_2018_gistic&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=acc_tcga_pan_can_atlas_2018_mutations&tab_index=tab_visualize`);
         waitForOncoprint(60000);
-        setOncoprintMutationsMenuOpen(true);
+        setResultsPageSettingsMenuOpen(true);
         browser.click('input[data-test="HideVUS"]');
+        setResultsPageSettingsMenuOpen(false);
         browser.waitForExist('a.tabAnchor_mutations');
         browser.click('a.tabAnchor_mutations');
         browser.waitForVisible('[data-test="LazyMobXTable_CountHeader"]');
         assert(browser.getHTML('[data-test="LazyMobXTable_CountHeader"]', false).indexOf("0 Mutations") > -1);
     });
+    it("uses germline filtering", function() {
+        goToUrlAndSetLocalStorage(`${CBIOPORTAL_URL}/results/mutations?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=brca_tcga_pub&case_set_id=brca_tcga_pub_cnaseq&data_priority=0&gene_list=BRCA1%2520BRCA2&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=brca_tcga_pub_gistic&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=brca_tcga_pub_mutations&tab_index=tab_visualize`);
+        browser.waitForVisible('[data-test="LazyMobXTable_CountHeader"]', 10000);
+        assert(browser.getHTML('[data-test="LazyMobXTable_CountHeader"]', false).indexOf("19 Mutations") > -1, "unfiltered is 19 mutations");
+
+        browser.click('button[data-test="GlobalSettingsButton"]');
+        browser.waitForVisible('div[data-test="GlobalSettingsDropdown"]', 10000);
+        browser.click('div[data-test="GlobalSettingsDropdown"] input[data-test="HideGermline"]');
+        browser.click('button[data-test="GlobalSettingsButton"]');
+
+        browser.waitForVisible('[data-test="LazyMobXTable_CountHeader"]', 10000);
+        assert(browser.getHTML('[data-test="LazyMobXTable_CountHeader"]', false).indexOf("6 Mutations") > -1, "filtered is 6 mutations");
+    });
 });
diff --git a/end-to-end-test/remote/specs/core/oncoprint.spec.js b/end-to-end-test/remote/specs/core/oncoprint.spec.js
diff --git a/end-to-end-test/shared/specUtils.js b/end-to-end-test/shared/specUtils.js
@@ -38,6 +38,20 @@ function getTextInOncoprintLegend() {
     return browser.getText("#oncoprintDiv .oncoprint-legend-div svg");
 }
 
+function setResultsPageSettingsMenuOpen(open) {
+    const button = 'button[data-test="GlobalSettingsButton"]';
+    const dropdown = 'div[data-test="GlobalSettingsDropdown"]';
+    browser.waitForVisible(button);
+    browser.waitUntil(()=>{
+        if (open === browser.isVisible(dropdown)) {
+            return true;
+        } else {
+            browser.click(button);
+            return false;
+        }
+    }, 10000, `Couldn't ${open ? "open" : "close"} results page settings menu`, 2000);
+}
+
 function setOncoprintMutationsMenuOpen(open) {
     const mutationColorMenuButton = "#mutationColorDropdown";
     const mutationColorMenuDropdown = "div.oncoprint__controls__mutation_color_menu";
@@ -317,5 +331,6 @@ module.exports = {
     selectCheckedOption: selectCheckedOption,
     getOncoprintGroupHeaderOptionsElements:getOncoprintGroupHeaderOptionsElements,
     showGsva: showGsva,
+    setResultsPageSettingsMenuOpen:setResultsPageSettingsMenuOpen,
     setDropdownOpen:setDropdownOpen
 };
diff --git a/src/pages/groupComparison/GroupComparisonStore.ts b/src/pages/groupComparison/GroupComparisonStore.ts
@@ -58,6 +58,7 @@ import {GACustomFieldsEnum, trackEvent} from "shared/lib/tracking";
 import ifndef from "../../shared/lib/ifndef";
 import {ISurvivalDescription} from "pages/resultsView/survival/SurvivalDescriptionTable";
 import GroupComparisonURLWrapper from "./GroupComparisonURLWrapper";
+import {CancerStudyQueryUrlParams} from "../../shared/components/query/QueryStore";
 import {fetchAllReferenceGenomeGenes} from "shared/lib/StoreUtils";
 
 export enum OverlapStrategy {

diff --git a/src/pages/resultsView/ResultsViewPageHelpers.ts b/src/pages/resultsView/ResultsViewPageHelpers.ts
@@ -1,16 +1,6 @@
 import * as _ from "lodash";
-import {getMolecularProfiles} from "./ResultsViewPageStoreUtils";
-import {runInAction} from "mobx";
-import {ResultsViewPageStore, SamplesSpecificationElement} from "./ResultsViewPageStore";
-import client from "../../shared/api/cbioportalClientInstance";
-import sessionServiceClient from "../../shared/api/sessionServiceInstance";
-import {CancerStudy} from "../../shared/api/generated/CBioPortalAPI";
+import {SamplesSpecificationElement} from "./ResultsViewPageStore";
 import {VirtualStudy} from "../../shared/model/VirtualStudy";
-import hashString from "../../shared/lib/hashString";
-import {
-    CLINICAL_TRACKS_URL_PARAM, HEATMAP_TRACKS_URL_PARAM,
-    SAMPLE_MODE_URL_PARAM
-} from "../../shared/components/oncoprint/ResultsViewOncoprint";
 
 export enum ResultsViewTab {
     ONCOPRINT="oncoprint",