Only use OQL filtering in mutations tab if theres mutation oql

Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
cBioPortal · Aug 15, 2018 · e1ca660 · e1ca660
1 parent da24bc6
commit e1ca660
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Showing 7 changed files with 59 additions and 8 deletions.
diff --git a/end-to-end-tests/specs/results.spec.js b/end-to-end-tests/specs/results.spec.js
@@ -158,6 +158,7 @@ describe('Results Page', function() {
     describe.only('oql status banner', function() {
         const yesBannerSelector = 'div[data-test="OqlStatusBannerYes"]';
         const noBannerSelector = 'div[data-test="OqlStatusBannerNo"]';
+        const unaffectedBannerSelector = 'div[data-test="OqlStatusBannerUnaffected"]';
         const simpleQueryUrl = `${CBIOPORTAL_URL}/index.do?cancer_study_id=coadread_tcga_pub&Z_SCORE_THRESHOLD=2&RPPA_SCORE_THRESHOLD=2&data_priority=0&case_set_id=coadread_tcga_pub_nonhypermut&gene_list=KRAS%2520NRAS%2520BRAF&geneset_list=+&tab_index=tab_visualize&Action=Submit&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=coadread_tcga_pub_mutations&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=coadread_tcga_pub_gistic`;
         const explicitOqlQueryUrl = `${CBIOPORTAL_URL}/index.do?cancer_study_id=coadread_tcga_pub&Z_SCORE_THRESHOLD=2&RPPA_SCORE_THRESHOLD=2&data_priority=0&case_set_id=coadread_tcga_pub_nonhypermut&gene_list=KRAS%2520NRAS%2520%250ABRAF%253AMUT&geneset_list=+&tab_index=tab_visualize&Action=Submit&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=coadread_tcga_pub_mutations&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=coadread_tcga_pub_gistic`;
 
@@ -190,6 +191,7 @@ describe('Results Page', function() {
             browser.pause(500);
             assert(!browser.isVisible(`${yesBannerSelector}.mutations-oql-status-banner`));
             assert(!browser.isVisible(`${noBannerSelector}.mutations-oql-status-banner`));
+            assert(!browser.isVisible(`${unaffectedBannerSelector}.mutations-oql-status-banner`));
         });
         it("should not be present in coexpression tab with simple query", function(){
             browser.click("#coexp-result-tab");
@@ -249,9 +251,10 @@ describe('Results Page', function() {
         });
         it("should be present in mutations tab with explicit query", function(){
             browser.click("#mutation-result-tab");
-            browser.waitForVisible(`${noBannerSelector}.mutations-oql-status-banner`, 10000);
-            assert(browser.isVisible(`${yesBannerSelector}.mutations-oql-status-banner`));
+            browser.waitForVisible(`${unaffectedBannerSelector}.mutations-oql-status-banner`, 10000);
+            assert(!browser.isVisible(`${yesBannerSelector}.mutations-oql-status-banner`));
             assert(!browser.isVisible(`${noBannerSelector}.mutations-oql-status-banner`));
+            assert(browser.isVisible(`${unaffectedBannerSelector}.mutations-oql-status-banner`));
         });
         it("should be present in coexpression tab with explicit query", function(){
             browser.click("#coexp-result-tab");

diff --git a/src/pages/resultsView/ResultsViewPageStore.ts b/src/pages/resultsView/ResultsViewPageStore.ts
@@ -43,6 +43,7 @@ import {
 import {writeTest} from "../../shared/lib/writeTest";
 import {PatientSurvival} from "../../shared/model/PatientSurvival";
 import {
+    doesQueryContainMutationOQL,
     doesQueryContainOQL,
     filterCBioPortalWebServiceData,
     filterCBioPortalWebServiceDataByOQLLine,
@@ -342,6 +343,10 @@ export class ResultsViewPageStore {
         return doesQueryContainOQL(this.oqlQuery);
     }
 
+    @computed get queryContainsMutationOql() {
+        return doesQueryContainMutationOQL(this.oqlQuery);
+    }
+
     private getURL() {
         const shareURL = window.location.href;
 
@@ -1177,11 +1182,12 @@ export class ResultsViewPageStore {
 
     });
 
-    @observable public mutationsTabUsingOql = true;
+    @observable public mutationsTabShouldUseOql = true;
 
     @computed get mutationsByGene():{ [hugeGeneSymbol:string]:Mutation[]}{
         let mutations:Mutation[];
-        if (this.mutationsTabUsingOql) {
+        if (this.mutationsTabShouldUseOql && this.queryContainsMutationOql) {
+            // use oql filtering in mutations tab only if query contains mutation oql
             mutations = (this.filteredAlterations.result || []).filter(a=>isMutation(a));
         } else {
             mutations = this.mutations.result || [];

diff --git a/src/pages/resultsView/mutation/Mutations.tsx b/src/pages/resultsView/mutation/Mutations.tsx
@@ -30,7 +30,7 @@ export default class Mutations extends React.Component<IMutationsPageProps, {}>
 
     @autobind
     private onToggleOql() {
-        this.props.store.mutationsTabUsingOql = !this.props.store.mutationsTabUsingOql;
+        this.props.store.mutationsTabShouldUseOql = !this.props.store.mutationsTabShouldUseOql;
     }
 
     public render() {
@@ -43,7 +43,8 @@ export default class Mutations extends React.Component<IMutationsPageProps, {}>
                 <OqlStatusBanner
                     className="mutations-oql-status-banner"
                     store={this.props.store}
-                    tabReflectsOql={this.props.store.mutationsTabUsingOql}
+                    tabReflectsOql={this.props.store.mutationsTabShouldUseOql}
+                    isUnaffected={!this.props.store.queryContainsMutationOql}
                     style={{marginTop:-2}}
                     onToggle={this.onToggleOql}
                 />

diff --git a/src/shared/components/oqlStatusBanner/OqlStatusBanner.tsx b/src/shared/components/oqlStatusBanner/OqlStatusBanner.tsx
@@ -8,6 +8,7 @@ import "./styles.scss";
 interface IOqlStatusBannerProps {
     store:ResultsViewPageStore;
     tabReflectsOql:boolean;
+    isUnaffected?:boolean;
     onToggle?:()=>void;
     className?:string;
     style?:any;
@@ -16,7 +17,7 @@ interface IOqlStatusBannerProps {
 @observer
 export default class OqlStatusBanner extends React.Component<IOqlStatusBannerProps, {}> {
     @computed get toggleButton() {
-        if (this.props.onToggle) {
+        if (this.props.onToggle && !this.props.isUnaffected) {
             return (
                 <span>
                     <button
@@ -47,7 +48,12 @@ export default class OqlStatusBanner extends React.Component<IOqlStatusBannerPro
             let iconClassName:string;
             let dataTest:string;
 
-            if (this.props.tabReflectsOql) {
+            if (this.props.isUnaffected) {
+                className="alert alert-unaffected";
+                message = "The results below are not affected by the OQL specification from your query.";
+                iconClassName = "fa fa-md fa-info-circle";
+                dataTest="OqlStatusBannerUnaffected";
+            } else if (this.props.tabReflectsOql) {
                 className="alert alert-success";
                 message = "The results below reflect the OQL specification from your query.";
                 iconClassName = "fa fa-md fa-check";

diff --git a/src/shared/components/oqlStatusBanner/styles.scss b/src/shared/components/oqlStatusBanner/styles.scss
@@ -2,4 +2,10 @@
   .banner-icon {
     vertical-align:middle !important;
   }
+
+  &.alert-unaffected {
+    background-color: #f3f3f3;
+    border-color: #bce8f1;
+    color: #31708f;
+  }
 }
diff --git a/src/shared/lib/oql/oqlfilter.d.ts b/src/shared/lib/oql/oqlfilter.d.ts
@@ -46,6 +46,10 @@ export declare function doesQueryContainOQL(
     oql_query:string
 ):boolean;
 
+export declare function doesQueryContainMutationOQL(
+    oql_query:string
+):boolean;
+
 export declare function filterCBioPortalWebServiceData(oql_query:string, data:(Mutation | NumericGeneMolecularData)[], accessors:any, default_oql:string): ExtendedAlteration[];
 
 export declare function filterCBioPortalWebServiceDataByOQLLine(oql_query:string, data:(AnnotatedMutation | NumericGeneMolecularData)[], accessors:any, default_oql:string): OQLLineFilterOutput<ExtendedAlteration&AnnotatedMutation>[];

diff --git a/src/shared/lib/oql/oqlfilter.js b/src/shared/lib/oql/oqlfilter.js
@@ -133,6 +133,31 @@ export function doesQueryContainOQL(oql_query) {
     return ret;
 }
 
+export function doesQueryContainMutationOQL(oql_query) {
+    /* In: oql_query, a string, an OQL query (which could just be genes with no specified alterations)
+     Out: boolean, true iff the query has explicit mutation OQL (e.g. `BRCA1: MISSENSE` as opposed to just `BRCA1` or `BRCA1: MUT`)
+     */
+
+    const parsedQuery = parseOQLQuery(oql_query);
+    let ret = false;
+    for (const singleGeneQuery of parsedQuery) {
+        if (singleGeneQuery.alterations !== false) {
+            for (const alteration of singleGeneQuery.alterations) {
+                if (alteration.alteration_type === "mut" &&
+                        alteration.constr_rel !== undefined) {
+                    // nontrivial mutation specification
+                    ret = true;
+                    break;
+                }
+            }
+            if (ret) {
+                break;
+            }
+        }
+    }
+    return ret;
+}
+
 var parsedOQLAlterationToSourceOQL = function(alteration) {
     if (alteration.alteration_type === "cna") {
         if (alteration.constr_rel === "=") {