Pass namespace columns as prop

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cBioPortal · Feb 3, 2022 · 1d654ca · 1d654ca
1 parent b9a1bfd
commit 1d654ca
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Showing 8 changed files with 78 additions and 21 deletions.
diff --git a/src/pages/patientView/PatientViewPage.tsx b/src/pages/patientView/PatientViewPage.tsx
@@ -80,6 +80,8 @@ import ClinicalEventsTables from './timeline2/ClinicalEventsTables';
 import MutationalSignaturesContainer from './mutationalSignatures/MutationalSignaturesContainer';
 import SampleSummaryList from './sampleHeader/SampleSummaryList';
 import { updateOncoKbIconStyle } from 'shared/lib/AnnotationColumnUtils';
+import { ExtendedMutationTableColumnType } from 'shared/components/mutationTable/MutationTable';
+import { extractColumnNames } from 'shared/components/mutationMapper/MutationMapperUtils';
 
 export interface IPatientViewPageProps {
     params: any; // react route
@@ -553,6 +555,16 @@ export default class PatientViewPage extends React.Component<
         this.patientViewPageStore.setMutationalSignaturesVersion(version);
     }
 
+    @computed get columns(): ExtendedMutationTableColumnType[] {
+        const namespaceColumnNames = extractColumnNames(
+            this.dataStore.namespaceColumnConfig
+        );
+        return _.concat(
+            PatientViewMutationTable.defaultProps.columns,
+            namespaceColumnNames
+        );
+    }
+
     public render() {
         let sampleManager: SampleManager | null = null;
         if (this.patientViewPageStore.sampleManager.isComplete) {
@@ -1224,6 +1236,7 @@ export default class PatientViewPage extends React.Component<
                                                         this.dataStore
                                                             .namespaceColumnConfig
                                                     }
+                                                    columns={this.columns}
                                                 />
                                             </div>
                                         )}

diff --git a/src/pages/patientView/mutation/PatientViewMutationTable.tsx b/src/pages/patientView/mutation/PatientViewMutationTable.tsx
@@ -396,13 +396,6 @@ export default class PatientViewMutationTable extends MutationTable<
         _.forIn(
             namespaceColumns,
             (column: MutationTableColumn, columnName: string) => {
-                if (
-                    this.props.columns &&
-                    !this.props.columns.includes(columnName)
-                ) {
-                    this.props.columns.push(columnName);
-                }
-
                 this._columns[columnName] = column;
             }
         );

diff --git a/src/pages/patientView/mutation/PatientViewMutationsTab.tsx b/src/pages/patientView/mutation/PatientViewMutationsTab.tsx
@@ -21,6 +21,13 @@ import WindowStore from '../../../shared/components/window/WindowStore';
 import VAFChartWrapper from 'pages/patientView/timeline2/VAFChartWrapper';
 import TimelineWrapper from 'pages/patientView/timeline2/TimelineWrapper';
 import VAFChartWrapperStore from '../timeline2/VAFChartWrapperStore';
+import { ExtendedMutationTableColumnType } from 'shared/components/mutationTable/MutationTable';
+import _ from 'lodash';
+import {
+    createNamespaceColumnName,
+    extractColumnNames,
+} from 'shared/components/mutationMapper/MutationMapperUtils';
+import ResultsViewMutationTable from 'pages/resultsView/mutation/ResultsViewMutationTable';
 
 export interface IPatientViewMutationsTabProps {
     patientViewPageStore: PatientViewPageStore;
@@ -350,11 +357,22 @@ export default class PatientViewMutationsTab extends React.Component<
                             .existsSomeMutationWithAscnProperty
                     }
                     namespaceColumns={this.dataStore.namespaceColumnConfig}
+                    columns={this.columns}
                 />
             </div>
         ),
     });
 
+    @computed get columns(): ExtendedMutationTableColumnType[] {
+        const namespaceColumnNames = extractColumnNames(
+            this.dataStore.namespaceColumnConfig
+        );
+        return _.concat(
+            PatientViewMutationTable.defaultProps.columns,
+            namespaceColumnNames
+        );
+    }
+
     readonly timeline = MakeMobxView({
         await: () => [this.props.patientViewPageStore.clinicalEvents],
         render: () => {

diff --git a/src/pages/resultsView/mutation/ResultsViewMutationMapper.tsx b/src/pages/resultsView/mutation/ResultsViewMutationMapper.tsx
@@ -42,6 +42,12 @@ import {
     getPatientSampleSummary,
     submitToStudyViewPage,
 } from '../querySummary/QuerySummaryUtils';
+import { ExtendedMutationTableColumnType } from 'shared/components/mutationTable/MutationTable';
+import {
+    buildNamespaceColumnConfig,
+    createNamespaceColumnName,
+    extractColumnNames,
+} from 'shared/components/mutationMapper/MutationMapperUtils';
 
 export interface IResultsViewMutationMapperProps extends IMutationMapperProps {
     store: ResultsViewMutationMapperStore;
@@ -252,10 +258,21 @@ export default class ResultsViewMutationMapper extends MutationMapper<
                 }
                 deactivateColumnFilter={this.deactivateColumnFilter}
                 namespaceColumns={this.props.store.namespaceColumnConfig}
+                columns={this.columns}
             />
         );
     }
 
+    @computed get columns(): ExtendedMutationTableColumnType[] {
+        const namespaceColumnNames = extractColumnNames(
+            this.props.store.namespaceColumnConfig
+        );
+        return _.concat(
+            ResultsViewMutationTable.defaultProps.columns,
+            namespaceColumnNames
+        );
+    }
+
     protected get mutationTable(): JSX.Element | null {
         return (
             <span>

diff --git a/src/pages/resultsView/mutation/ResultsViewMutationTable.tsx b/src/pages/resultsView/mutation/ResultsViewMutationTable.tsx
@@ -183,13 +183,6 @@ export default class ResultsViewMutationTable extends MutationTable<
         _.forIn(
             namespaceColumns,
             (column: MutationTableColumn, columnName: string) => {
-                if (
-                    this.props.columns &&
-                    !this.props.columns.includes(columnName)
-                ) {
-                    this.props.columns.push(columnName);
-                }
-
                 this._columns[columnName] = column;
             }
         );

diff --git a/src/pages/staticPages/tools/mutationMapper/StandaloneMutationMapper.tsx b/src/pages/staticPages/tools/mutationMapper/StandaloneMutationMapper.tsx
@@ -7,6 +7,14 @@ import {
 } from 'shared/components/mutationMapper/MutationMapper';
 import { MutationTableDownloadDataFetcher } from 'shared/lib/MutationTableDownloadDataFetcher';
 import MutationMapperDataStore from 'shared/components/mutationMapper/MutationMapperDataStore';
+import { computed } from 'mobx';
+import { ExtendedMutationTableColumnType } from 'shared/components/mutationTable/MutationTable';
+import _ from 'lodash';
+import {
+    createNamespaceColumnName,
+    extractColumnNames,
+} from 'shared/components/mutationMapper/MutationMapperUtils';
+import ResultsViewMutationTable from 'pages/resultsView/mutation/ResultsViewMutationTable';
 
 export interface IStandaloneMutationMapperProps extends IMutationMapperProps {
     // add standalone view specific props here if needed
@@ -64,10 +72,21 @@ export default class StandaloneMutationMapper extends MutationMapper<
                 }
                 selectedTranscriptId={this.props.store.activeTranscript.result}
                 namespaceColumns={this.props.store.namespaceColumnConfig}
+                columns={this.columns}
             />
         );
     }
 
+    @computed get columns(): ExtendedMutationTableColumnType[] {
+        const namespaceColumnNames = extractColumnNames(
+            this.props.store.namespaceColumnConfig
+        );
+        return _.concat(
+            StandaloneMutationTable.defaultProps.columns,
+            namespaceColumnNames
+        );
+    }
+
     protected get isMutationTableDataLoading() {
         return this.props.store.activeTranscript.isPending;
     }

diff --git a/src/pages/staticPages/tools/mutationMapper/StandaloneMutationTable.tsx b/src/pages/staticPages/tools/mutationMapper/StandaloneMutationTable.tsx
@@ -65,13 +65,6 @@ export default class StandaloneMutationTable extends MutationTable<
         _.forIn(
             namespaceColumns,
             (column: MutationTableColumn, columnName: string) => {
-                if (
-                    this.props.columns &&
-                    !this.props.columns.includes(columnName)
-                ) {
-                    this.props.columns.push(columnName);
-                }
-
                 this._columns[columnName] = column;
             }
         );

diff --git a/src/shared/components/mutationMapper/MutationMapperUtils.ts b/src/shared/components/mutationMapper/MutationMapperUtils.ts
@@ -63,6 +63,17 @@ export function createNamespaceColumnName(
     return namespaceName + ' ' + _.capitalize(namespaceColumnName);
 }
 
+export function extractColumnNames(config: NamespaceColumnConfig): string[] {
+    return _.flatMap(config, (namespaceCol, namespaceName) =>
+        _.keys(namespaceCol).map(namespaceColumnName =>
+            createNamespaceColumnName(
+                namespaceName.toString(),
+                namespaceColumnName
+            )
+        )
+    );
+}
+
 function fMerge(refObject: any, addedObject: any) {
     if (_.isArray(refObject)) {
         return refObject.concat(addedObject);