Merge pull request #2726 from alisman/urlWrapper

Url wrapper
cBioPortal · Dec 6, 2019 · eceb5f8 · eceb5f8
2 parents 31a57ae + 72f52d2
commit eceb5f8
Show file tree

Hide file tree

Showing 44 changed files with 1,775 additions and 1,219 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -35,6 +35,7 @@ run_e2e_and_save_artifacts: &run_e2e_and_save_artifacts
           (curl --insecure https://localhost:3000 || curl http://localhost:3000) > /dev/null && \
           sleep 1s && \
           cd end-to-end-test && \
+          echo "CBIOPORTAL_URL=$CBIOPORTAL_URL"
           yarn run e2e
         when: always
         environment:
@@ -199,14 +200,14 @@ jobs:
               ./setup_environment.sh && ./setup_environment.sh >> $BASH_ENV
       - run:
           name: Generate checksum of data that populates the test database
-          command: |         
+          command: |
               $TEST_HOME/local/runtime-config/db_content_fingerprint.sh > /tmp/db_data_md5key
       - restore_cache:
           keys:
           - v4-e2e-database-files-{{ checksum "/tmp/db_data_md5key" }}
       - run:
           name: Create MySQL data directory when no cache found
-          command: |         
+          command: |
               mkdir -p $DB_DATA_DIR
       - run:
           name: Setup docker images and containers
@@ -220,7 +221,7 @@ jobs:
               fi
       - run:
           name: Change owner of MySQL database files (needed by cache)
-          command: |         
+          command: |
               sudo chmod -R 777 $DB_DATA_DIR && \
               sudo chown -R circleci:circleci $DB_DATA_DIR
       - save_cache:
@@ -229,7 +230,7 @@ jobs:
           key: v4-e2e-database-files-{{ checksum "/tmp/db_data_md5key" }}
       - run:
           name: Run end-2-end tests with studies in local database
-          command: | 
+          command: |
               cd $PORTAL_SOURCE_DIR && $TEST_HOME/local/runtime-config/run_container_screenshot_test.sh
       - run:
           name: "Make sure all screenshots are tracked (otherwise the test will always be successful)"

diff --git a/...eference/acc_tcga_with_clinical_and_heatmap_tracks_element_chrome_1600x1000.png b/...eference/acc_tcga_with_clinical_and_heatmap_tracks_element_chrome_1600x1000.png
diff --git a/...ference/blca_tcga_with_clinical_and_heatmap_tracks_element_chrome_1600x1000.png b/...ference/blca_tcga_with_clinical_and_heatmap_tracks_element_chrome_1600x1000.png
diff --git a/...coadread_tcga_pub_with_clinical_and_heatmap_tracks_element_chrome_1600x1000.png b/...coadread_tcga_pub_with_clinical_and_heatmap_tracks_element_chrome_1600x1000.png
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/src/appShell/App/Container.tsx b/src/appShell/App/Container.tsx
@@ -41,12 +41,6 @@ export default class Container extends React.Component<IContainerProps, {}> {
             c => React.cloneElement(c as React.ReactElement<any>, childProps));
     }
 
-    @computed get isSessionLoaded(){
-
-        return !this.routingStore.needsRemoteSessionLookup || this.routingStore.remoteSessionData.isComplete;
-
-    }
-
     render() {
         if (!isWebdriver() && !ServerConfigHelpers.sessionServiceIsEnabled()) {
             return (
@@ -61,44 +55,37 @@ export default class Container extends React.Component<IContainerProps, {}> {
         }
 
         return (
-            <If condition={this.isSessionLoaded}>
-                <div>
-                    <Helmet>
-                        <meta charSet="utf-8" />
-                        <title>{AppConfig.serverConfig.skin_title}</title>
-                        <meta name="description" content={AppConfig.serverConfig.skin_description} />
-                    </Helmet>
-
-                    <div className="pageTopContainer">
-                        <UserMessager />
-                        <div className="contentWidth">
-                            <PortalHeader appStore={this.appStore}/>
-                        </div>
+            <div>
+                <Helmet>
+                    <meta charSet="utf-8" />
+                    <title>{AppConfig.serverConfig.skin_title}</title>
+                    <meta name="description" content={AppConfig.serverConfig.skin_description} />
+                </Helmet>
+
+                <div className="pageTopContainer">
+                    <UserMessager />
+                    <div className="contentWidth">
+                        <PortalHeader appStore={this.appStore}/>
                     </div>
-                    <If condition={this.appStore.isErrorCondition}>
-                        <Then>
-                            <div className="contentWrapper">
-                                <ErrorScreen
-                                    title={formatErrorTitle(this.appStore.undismissedSiteErrors) || "Oops. There was an error retrieving data."}
-                                    body={<a href={buildCBioPortalPageUrl("/")}>Return to homepage</a>}
-                                    errorLog={formatErrorLog(this.appStore.undismissedSiteErrors)}
-                                    errorMessages={formatErrorMessages(this.appStore.undismissedSiteErrors)}
-                                />
-                            </div>
-                        </Then>
-                        <Else>
-                            <div className="contentWrapper">
-                                {(this.isSessionLoaded) && this.props.children}
-                            </div>
-                        </Else>
-                    </If>
-
-
                 </div>
-                <Else>
-                    <LoadingIndicator isLoading={!this.isSessionLoaded} center={true} size={"big"}/>
-                </Else>
-            </If>
+                <If condition={this.appStore.isErrorCondition}>
+                    <Then>
+                        <div className="contentWrapper">
+                            <ErrorScreen
+                                title={formatErrorTitle(this.appStore.undismissedSiteErrors) || "Oops. There was an error retrieving data."}
+                                body={<a href={buildCBioPortalPageUrl("/")}>Return to homepage</a>}
+                                errorLog={formatErrorLog(this.appStore.undismissedSiteErrors)}
+                                errorMessages={formatErrorMessages(this.appStore.undismissedSiteErrors)}
+                            />
+                        </div>
+                    </Then>
+                    <Else>
+                        <div className="contentWrapper">
+                            {this.props.children}
+                        </div>
+                    </Else>
+                </If>
+            </div>
         );
     }
 }

diff --git a/src/config/serverConfigDefaults.ts b/src/config/serverConfigDefaults.ts
@@ -105,7 +105,7 @@ const ServerConfigDefaults: Partial<IServerConfig> = {
 
     enable_darwin: false,
 
-    session_url_length_threshold: '1990',
+    session_url_length_threshold: '1500',
 
     study_view: {
         tableAttrs: ['SAMPLE_CANCER_TYPE', 'SAMPLE_CANCER_TYPE_DETAILED'],
@@ -156,7 +156,7 @@ const ServerConfigDefaults: Partial<IServerConfig> = {
         'http://grch37.ensembl.org/homo_sapiens/Transcript/Summary?t=<%= transcriptId %>',
 
     query_product_limit: 1000000,
-    
+
     skin_show_gsva: false,
 };
 

diff --git a/src/pages/groupComparison/GroupComparisonPage.tsx b/src/pages/groupComparison/GroupComparisonPage.tsx
@@ -80,6 +80,7 @@ export default class GroupComparisonPage extends React.Component<IGroupCompariso
     componentWillUnmount() {
         this.queryReaction && this.queryReaction();
         this.store && this.store.destroy();
+        this.urlWrapper.destroy();
     }
 
     readonly tabs = MakeMobxView({

diff --git a/src/pages/groupComparison/GroupComparisonStore.ts b/src/pages/groupComparison/GroupComparisonStore.ts
@@ -106,7 +106,7 @@ export default class GroupComparisonStore {
     }
 
     @action public updateOverlapStrategy(strategy:OverlapStrategy) {
-        this.urlWrapper.updateQuery({ overlapStrategy: strategy });
+        this.urlWrapper.updateURL({ overlapStrategy: strategy });
     }
 
     @computed get overlapStrategy() {
@@ -120,7 +120,7 @@ export default class GroupComparisonStore {
 
     @autobind
     @action public setUsePatientLevelEnrichments(e:boolean) {
-        this.urlWrapper.updateQuery({ patientEnrichments: e.toString()});
+        this.urlWrapper.updateURL({ patientEnrichments: e.toString()});
     }
 
     @computed get groupOrder() {
@@ -141,11 +141,11 @@ export default class GroupComparisonStore {
         const poppedUid = groupOrder.splice(oldIndex, 1)[0];
         groupOrder.splice(newIndex, 0, poppedUid);
 
-        this.urlWrapper.updateQuery({ groupOrder: JSON.stringify(groupOrder) });
+        this.urlWrapper.updateURL({ groupOrder: JSON.stringify(groupOrder) });
     }
 
     @action private updateUnselectedGroups(names:string[]) {
-        this.urlWrapper.updateQuery({ unselectedGroups: JSON.stringify(names) });
+        this.urlWrapper.updateURL({ unselectedGroups: JSON.stringify(names) });
     }
 
     @computed get unselectedGroups() {
@@ -210,7 +210,7 @@ export default class GroupComparisonStore {
     @action
     private async saveAndGoToSession(newSession:Session) {
         const {id} = await comparisonClient.addComparisonSession(newSession);
-        this.urlWrapper.updateQuery({ sessionId: id});
+        this.urlWrapper.updateURL({ sessionId: id});
     }
 
     readonly _session = remoteData<Session>({

diff --git a/src/pages/groupComparison/GroupComparisonURLWrapper.ts b/src/pages/groupComparison/GroupComparisonURLWrapper.ts
@@ -30,6 +30,6 @@ export default class GroupComparisonURLWrapper extends URLWrapper<GroupCompariso
 
     @autobind
     public setTabId(tabId:GroupComparisonTab, replace?:boolean) {
-        this.routing.updateRoute({}, `comparison/${tabId}`, false, replace);
+        this.updateURL({}, `comparison/${tabId}`, false, replace);
     }
-}
+}
diff --git a/src/pages/groupComparison/Survival.tsx b/src/pages/groupComparison/Survival.tsx
@@ -1,5 +1,6 @@
 import * as React from 'react';
 import SurvivalChart from "../resultsView/survival/SurvivalChart";
+import 'react-rangeslider/lib/index.css';
 import LoadingIndicator from "shared/components/loadingIndicator/LoadingIndicator";
 import {observer} from "mobx-react";
 import GroupComparisonStore, {OverlapStrategy} from './GroupComparisonStore';
@@ -11,9 +12,6 @@ import {blendColors} from "./OverlapUtils";
 import OverlapExclusionIndicator from "./OverlapExclusionIndicator";
 import {getPatientIdentifiers} from "../studyView/StudyViewUtils";
 import DefaultTooltip from 'public-lib/components/defaultTooltip/DefaultTooltip';
-import classnames from 'classnames';
-import styles from "./styles.module.scss";
-import { ClinicalData, ClinicalAttribute } from 'shared/api/generated/CBioPortalAPI';
 import _ from 'lodash';
 import SurvivalDescriptionTable from 'pages/resultsView/survival/SurvivalDescriptionTable';
 import {

diff --git a/src/pages/home/HomePage.tsx b/src/pages/home/HomePage.tsx
@@ -14,6 +14,9 @@ import getBrowserWindow from "../../public-lib/lib/getBrowserWindow";
 // tslint:disable-next-line:no-import-side-effect
 import "./homePage.scss";
 import autobind from "autobind-decorator";
+import {ResultsViewTab} from "pages/resultsView/ResultsViewPageHelpers";
+import ResultsViewURLWrapper from "pages/resultsView/ResultsViewURLWrapper";
+import {createQueryStore} from "shared/lib/createQueryStore";
 
 (Chart as any).plugins.register({
     beforeDraw: function (chartInstance: any) {
@@ -29,25 +32,6 @@ export interface IResultsViewPageProps {
     routing: any;
 }
 
-export function createQueryStore(currentQuery?:any) {
-
-    const win:any = window;
-
-    const queryStore = new QueryStore(currentQuery);
-
-    queryStore.singlePageAppSubmitRoutine = function(query:CancerStudyQueryUrlParams) {
-
-        // normalize this
-        query.cancer_study_list = query.cancer_study_list || query.cancer_study_id;
-        delete query.cancer_study_id;
-
-        win.routingStore.updateRoute(query, "results", true);
-
-    };
-
-    return queryStore;
-
-}
 
 @inject('routing')
 @observer

diff --git a/src/pages/patientView/PatientViewPage.spec.tsx b/src/pages/patientView/PatientViewPage.spec.tsx
@@ -2,37 +2,32 @@ import  PatientViewPage from './PatientViewPage';
 import React from 'react';
 import {assert} from 'chai';
 import sinon from 'sinon';
-import PatientViewUrlWrapper from './PatientViewUrlWrapper';
-import ExtendedRouterStore from 'shared/lib/ExtendedRouterStore';
 
 const componentUnderTest: PatientViewPage = (PatientViewPage as any).wrappedComponent;
 
-
 describe('PatientViewPage', () => {
 
     describe('handleSampleClick', () => {
 
         const handleSampleClick = (componentUnderTest as any).prototype.handleSampleClick;
 
-        let updateRouteStub: sinon.SinonStub,
-        urlWrapper: PatientViewUrlWrapper,
-        preventDefaultStub: sinon.SinonStub,
-        mock: any,
-        ev: Partial<React.MouseEvent<HTMLAnchorElement>>;
+        let updateURLStub:sinon.SinonStub,
+            preventDefaultStub: sinon.SinonStub,
+            mock: any,
+            ev: Partial<React.MouseEvent<HTMLAnchorElement>>;
+
+
 
         beforeEach(() => {
-            updateRouteStub = sinon.stub();
-            urlWrapper = new PatientViewUrlWrapper(new ExtendedRouterStore());
-            urlWrapper.updateQuery = updateRouteStub;
+
+            updateURLStub = sinon.stub();
+
             preventDefaultStub = sinon.stub();
 
             mock = {
-                props: {
-                    routing: {
-                        updateRoute: updateRouteStub
-                    }
-                },
-                urlWrapper: urlWrapper,
+                urlWrapper: {
+                    updateURL:updateURLStub
+                }
             };
 
             ev = {
@@ -43,29 +38,29 @@ describe('PatientViewPage', () => {
 
         it('calls update route when no modifier keys are pressed', () => {
             handleSampleClick.call(mock, 1, ev);
-            assert.isTrue(updateRouteStub.calledOnce);
+            assert.isTrue(updateURLStub.calledOnce);
             assert.isTrue(preventDefaultStub.called);
         });
 
         it('does not call updateRoute or preventDefault if altKey is true', () => {
             ev.altKey = true;
             handleSampleClick.call(mock, 1, ev);
-            assert.isFalse(updateRouteStub.called);
+            assert.isFalse(updateURLStub.called);
             assert.isFalse(preventDefaultStub.called);
         });
 
 
         it('does not call updateRoute or preventDefault if metaKey is true', () => {
             ev.metaKey = true;
             handleSampleClick.call(mock, 1, ev);
-            assert.isFalse(updateRouteStub.called);
+            assert.isFalse(updateURLStub.called);
             assert.isFalse(preventDefaultStub.called);
         });
 
         it('does not call updateRoute or preventDefault if shiftKey is true', () => {
             ev.shiftKey = true;
             handleSampleClick.call(mock, 1, ev);
-            assert.isFalse(updateRouteStub.called);
+            assert.isFalse(updateURLStub.called);
             assert.isFalse(preventDefaultStub.called);
         });