add missing columns in the mutation mapper table

cBioPortal · Nov 29, 2019 · 33f917c · 33f917c
1 parent fe241c4
commit 33f917c
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Showing 4 changed files with 11 additions and 1 deletion.
diff --git a/src/pages/staticPages/tools/mutationMapper/MutationMapperTool.tsx b/src/pages/staticPages/tools/mutationMapper/MutationMapperTool.tsx
@@ -379,6 +379,7 @@ export default class MutationMapperTool extends React.Component<IMutationMapperT
                             trackVisibility={this.userSelectionStore.trackVisibility}
                             downloadDataFetcher={this.store.downloadDataFetcher}
                             genomeNexusCache={this.store.genomeNexusCache}
+                            genomeNexusMyVariantInfoCache={this.store.genomeNexusMyVariantInfoCache}
                             oncoKbEvidenceCache={this.store.oncoKbEvidenceCache}
                             pubMedCache={this.store.pubMedCache}
                             pdbHeaderCache={this.store.pdbHeaderCache}

diff --git a/src/pages/staticPages/tools/mutationMapper/StandaloneMutationMapper.tsx b/src/pages/staticPages/tools/mutationMapper/StandaloneMutationMapper.tsx
@@ -26,6 +26,7 @@ export default class StandaloneMutationMapper extends MutationMapper<IStandalone
                 oncoKbCancerGenes={this.props.store.oncoKbCancerGenes}
                 indexedVariantAnnotations={this.props.store.indexedVariantAnnotations}
                 genomeNexusCache={this.props.genomeNexusCache}
+                genomeNexusMyVariantInfoCache={this.props.genomeNexusMyVariantInfoCache}
                 oncoKbEvidenceCache={this.props.oncoKbEvidenceCache}
                 pubMedCache={this.props.pubMedCache}
                 dataStore={this.props.store.dataStore}

diff --git a/src/pages/staticPages/tools/mutationMapper/StandaloneMutationTable.tsx b/src/pages/staticPages/tools/mutationMapper/StandaloneMutationTable.tsx
@@ -40,7 +40,10 @@ export default class StandaloneMutationTable extends MutationTable<IStandaloneMu
             MutationTableColumnType.PROTEIN_CHANGE,
             MutationTableColumnType.MUTATION_TYPE,
             MutationTableColumnType.TUMOR_ALLELE_FREQ,
-            MutationTableColumnType.NORMAL_ALLELE_FREQ
+            MutationTableColumnType.NORMAL_ALLELE_FREQ,
+            MutationTableColumnType.HGVSC,
+            MutationTableColumnType.GNOMAD,
+            MutationTableColumnType.CLINVAR
         ]
     };
 
@@ -80,5 +83,8 @@ export default class StandaloneMutationTable extends MutationTable<IStandaloneMu
         this._columns[MutationTableColumnType.VAR_READS_N].order = 200;
         this._columns[MutationTableColumnType.REF_READS_N].order = 210;
         //this._columns[MutationTableColumnType.NUM_MUTATIONS].order = 220;
+        this._columns[MutationTableColumnType.HGVSC].order = 220;
+        this._columns[MutationTableColumnType.GNOMAD].order = 230;
+        this._columns[MutationTableColumnType.CLINVAR].order = 240;
     }
 }
diff --git a/src/shared/components/mutationMapper/MutationMapper.tsx b/src/shared/components/mutationMapper/MutationMapper.tsx
@@ -25,6 +25,7 @@ import StructureViewerPanel from "shared/components/structureViewer/StructureVie
 import OncoKbEvidenceCache from "shared/cache/OncoKbEvidenceCache";
 import PubMedCache from "shared/cache/PubMedCache";
 import GenomeNexusCache from "shared/cache/GenomeNexusCache";
+import GenomeNexusMyVariantInfoCache from 'shared/cache/GenomeNexusMyVariantInfoCache';
 import {IMyCancerGenomeData} from "shared/model/MyCancerGenome";
 import PdbHeaderCache from "shared/cache/PdbHeaderCache";
 import {DEFAULT_PROTEIN_IMPACT_TYPE_COLORS, getColorForProteinImpactType} from "shared/lib/MutationUtils";
@@ -53,6 +54,7 @@ export interface IMutationMapperProps {
     pdbHeaderCache?: PdbHeaderCache;
     oncoKbEvidenceCache?:OncoKbEvidenceCache;
     genomeNexusCache?:GenomeNexusCache;
+    genomeNexusMyVariantInfoCache?:GenomeNexusMyVariantInfoCache;
     // server config properties
     genomeNexusUrl?: string;
     oncoKbPublicApiUrl?: string;