Fix mutational sig bug when no count data is present

Fix cBioPortal/cbioportal#10538. This is a fix for studies when only mutational signatures contribution and p-values are loaded (and no mutational signatures count data)
cBioPortal · Jul 3, 2024 · 0ab0f9b · 0ab0f9b
1 parent 126167e
commit 0ab0f9b
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diff --git a/...creenshots/reference/show_mutational_bar_chart_dbs_element_chrome_1600x1000.png b/...creenshots/reference/show_mutational_bar_chart_dbs_element_chrome_1600x1000.png
diff --git a/...screenshots/reference/show_mutational_bar_chart_id_element_chrome_1600x1000.png b/...screenshots/reference/show_mutational_bar_chart_id_element_chrome_1600x1000.png
diff --git a/...creenshots/reference/show_mutational_bar_chart_sbs_element_chrome_1600x1000.png b/...creenshots/reference/show_mutational_bar_chart_sbs_element_chrome_1600x1000.png
diff --git a/...able_for_patient_who_has_significant_id_signatures_element_chrome_1600x1000.png b/...able_for_patient_who_has_significant_id_signatures_element_chrome_1600x1000.png
diff --git a/...ble_for_patient_who_has_significant_sbs_signatures_element_chrome_1600x1000.png b/...ble_for_patient_who_has_significant_sbs_signatures_element_chrome_1600x1000.png
diff --git a/...rence/show_the_bar_chart_with_percentage_on_y_axis_element_chrome_1600x1000.png b/...rence/show_the_bar_chart_with_percentage_on_y_axis_element_chrome_1600x1000.png
diff --git a/...tip_for_patient_who_has_significant_dbs_signatures_element_chrome_1600x1000.png b/...tip_for_patient_who_has_significant_dbs_signatures_element_chrome_1600x1000.png
diff --git a/...ltip_for_patient_who_has_significant_id_signatures_element_chrome_1600x1000.png b/...ltip_for_patient_who_has_significant_id_signatures_element_chrome_1600x1000.png
diff --git a/...tip_for_patient_who_has_significant_sbs_signatures_element_chrome_1600x1000.png b/...tip_for_patient_who_has_significant_sbs_signatures_element_chrome_1600x1000.png
diff --git a/...tch_between_samples_to_update_mutational_bar_chart_element_chrome_1600x1000.png b/...tch_between_samples_to_update_mutational_bar_chart_element_chrome_1600x1000.png
diff --git a/src/pages/patientView/PatientViewPageTabs.tsx b/src/pages/patientView/PatientViewPageTabs.tsx
@@ -645,58 +645,61 @@ export function tabs(
             </MSKTab>
         );
 
-    tabs.push(
-        <MSKTab
-            key={8}
-            id="mutationalSignatures"
-            linkText="Mutational Signatures"
-            hide={
-                pageComponent.patientViewPageStore
-                    .mutationalSignatureMolecularProfiles.isPending ||
-                pageComponent.patientViewPageStore
-                    .initialMutationalSignatureVersion.isPending ||
-                _.isEmpty(
-                    pageComponent.patientViewPageStore
-                        .mutationalSignatureDataGroupByVersion.result
-                )
-            }
-        >
-            <MutationalSignaturesContainer
-                data={
-                    pageComponent.patientViewPageStore
-                        .mutationalSignatureDataGroupByVersion.result
-                }
-                profiles={
-                    pageComponent.patientViewPageStore
-                        .mutationalSignatureMolecularProfiles.result
-                }
-                onVersionChange={
-                    pageComponent.onMutationalSignatureVersionChange
-                }
-                version={
-                    pageComponent.patientViewPageStore
-                        .selectedMutationalSignatureVersion
-                }
-                dataCount={
-                    pageComponent.patientViewPageStore
-                        .mutationalSignatureCountDataGroupedByVersion.result
-                }
-                sample={
-                    pageComponent.patientViewPageStore
-                        .selectedSampleMutationalSignatureData
-                }
-                samples={
+    pageComponent.patientViewPageStore.hasMutationalSignatureData.result &&
+        pageComponent.patientViewPageStore.initialMutationalSignatureVersion
+            .isComplete &&
+        tabs.push(
+            <MSKTab
+                key={8}
+                id="mutationalSignatures"
+                linkText="Mutational Signatures"
+                hide={
                     pageComponent.patientViewPageStore
-                        .samplesWithCountDataAvailable
-                }
-                samplesNotProfiled={
+                        .mutationalSignatureMolecularProfiles.isPending ||
                     pageComponent.patientViewPageStore
-                        .samplesNotProfiledForMutationalSignatures
+                        .initialMutationalSignatureVersion.isPending ||
+                    _.isEmpty(
+                        pageComponent.patientViewPageStore
+                            .mutationalSignatureDataGroupByVersion.result
+                    )
                 }
-                onSampleChange={pageComponent.onSampleIdChange}
-            />
-        </MSKTab>
-    );
+            >
+                <MutationalSignaturesContainer
+                    data={
+                        pageComponent.patientViewPageStore
+                            .mutationalSignatureDataGroupByVersion.result
+                    }
+                    profiles={
+                        pageComponent.patientViewPageStore
+                            .mutationalSignatureMolecularProfiles.result
+                    }
+                    onVersionChange={
+                        pageComponent.onMutationalSignatureVersionChange
+                    }
+                    version={
+                        pageComponent.patientViewPageStore
+                            .selectedMutationalSignatureVersion
+                    }
+                    dataCount={
+                        pageComponent.patientViewPageStore
+                            .mutationalSignatureCountDataGroupedByVersion.result
+                    }
+                    sample={
+                        pageComponent.patientViewPageStore
+                            .selectedSampleMutationalSignatureData
+                    }
+                    samples={
+                        pageComponent.patientViewPageStore
+                            .samplesWithDataAvailable
+                    }
+                    samplesNotProfiled={
+                        pageComponent.patientViewPageStore
+                            .samplesNotProfiledForMutationalSignatures
+                    }
+                    onSampleChange={pageComponent.onSampleIdChange}
+                />
+            </MSKTab>
+        );
 
     pageComponent.resourceTabs.component &&
         /* @ts-ignore */

diff --git a/src/pages/patientView/PatientViewPageUtils.tsx b/src/pages/patientView/PatientViewPageUtils.tsx
@@ -10,10 +10,7 @@ import {
     IMutationalSignatureMeta,
     IMutationalCounts,
 } from 'shared/model/MutationalSignature';
-import {
-    getGenericAssayMetaPropertyOrDefault,
-    getGenericAssayCategoryFromName,
-} from 'shared/lib/GenericAssayUtils/GenericAssayCommonUtils';
+import { getGenericAssayMetaPropertyOrDefault } from 'shared/lib/GenericAssayUtils/GenericAssayCommonUtils';
 import {
     MutationalSignatureLabelMap,
     MutationalSignatureCount,

diff --git a/...ages/patientView/clinicalInformation/ClinicalInformationMutationalSignatureTable.spec.tsx b/...ages/patientView/clinicalInformation/ClinicalInformationMutationalSignatureTable.spec.tsx
@@ -8,7 +8,7 @@ const sampleMutationalSignatureMeta = [
     {
         mutationalSignatureId: 'firstMutationalSignature',
         name: 'Mutational Signature 1',
-        description: 'Mutational Signature 1',
+        description: 'Description Signature 1',
         url: 'COSMIC/FakeMutationalSignature1',
         category: 'category 1',
         confidenceStatement:
@@ -17,7 +17,7 @@ const sampleMutationalSignatureMeta = [
     {
         mutationalSignatureId: 'secondMutationalSignature',
         name: 'Mutational Signature 2',
-        description: 'Mutational Signature 2',
+        description: 'Description Signature 2',
         url: 'COSMIC/FakeMutationalSignature2',
         category: 'category 2',
         confidenceStatement:
@@ -99,6 +99,7 @@ describe('ClinicalInformationMutationalSignatureTable', () => {
                         confidence: 0.8,
                     },
                 },
+                description: 'Description Signature 1',
                 url: 'COSMIC/FakeMutationalSignature1',
             },
             {
@@ -113,6 +114,7 @@ describe('ClinicalInformationMutationalSignatureTable', () => {
                         confidence: 0.01,
                     },
                 },
+                description: 'Description Signature 2',
                 url: 'COSMIC/FakeMutationalSignature2',
             },
         ]);

diff --git a/src/pages/patientView/clinicalInformation/ClinicalInformationMutationalSignatureTable.tsx b/src/pages/patientView/clinicalInformation/ClinicalInformationMutationalSignatureTable.tsx
@@ -34,6 +34,7 @@ export interface IMutationalSignatureRow {
             confidence: number;
         };
     };
+    description: string;
     url: string;
 }
 
@@ -74,15 +75,29 @@ export default class ClinicalInformationMutationalSignatureTable extends React.C
                         <b>Signature: </b>
                         {this.props.signature}
                     </h5>
-                    <p style={{ fontSize: '12px' }}>
-                        <b>Description: </b>
-                        {this.props.description}
-                    </p>
-                    <p style={{ fontSize: '12px' }}>
-                        <a href={this.props.url} target="_blank">
-                            External link to signature (opens new tab)
-                        </a>
-                    </p>
+                    {this.props.description != '' && (
+                        <p style={{ fontSize: '12px' }}>
+                            <b>Description: </b>
+                            {this.props.description}
+                        </p>
+                    )}
+                    {this.props.description == '' && (
+                        <p style={{ fontSize: '12px' }}>
+                            No description annnotated in data
+                        </p>
+                    )}
+                    {this.props.url != '' && (
+                        <p style={{ fontSize: '12px' }}>
+                            <a href={this.props.url} target="_blank">
+                                External link to signature (opens new tab)
+                            </a>
+                        </p>
+                    )}
+                    {this.props.url == '' && (
+                        <p style={{ fontSize: '12px' }}>
+                            No url annnotated in data
+                        </p>
+                    )}
                 </div>
             </div>
         );

diff --git a/src/pages/patientView/clinicalInformation/PatientViewPageStore.ts b/src/pages/patientView/clinicalInformation/PatientViewPageStore.ts
@@ -902,12 +902,17 @@ export class PatientViewPageStore {
             .filter(item => item.sampleId === sampleToFilter)
             .map(item => item.uniqueSampleKey);
     }
-    @computed get samplesWithCountDataAvailable(): string[] {
+
+    @computed get samplesWithDataAvailable(): string[] {
         return this.fetchAllMutationalSignatureData.result
-            .filter(data =>
-                data.molecularProfileId.includes(
-                    MutationalSignatureStableIdKeyWord.MutationalSignatureCountKeyWord
-                )
+            .filter(
+                data =>
+                    data.molecularProfileId.includes(
+                        MutationalSignatureStableIdKeyWord.MutationalSignatureCountKeyWord
+                    ) ||
+                    data.molecularProfileId.includes(
+                        MutationalSignatureStableIdKeyWord.MutationalSignatureContributionKeyWord
+                    )
             )
             .map(sample => sample.sampleId)
             .filter((value, index, self) => self.indexOf(value) === index);
@@ -918,7 +923,7 @@ export class PatientViewPageStore {
             sample => sample.sampleId
         );
         return allSamples.filter(
-            element => !this.samplesWithCountDataAvailable.includes(element)
+            element => !this.samplesWithDataAvailable.includes(element)
         );
     }
 

diff --git a/src/pages/patientView/mutationalSignatures/MutationalSignatureBarChartUtils.ts b/src/pages/patientView/mutationalSignatures/MutationalSignatureBarChartUtils.ts
@@ -547,17 +547,21 @@ export function prepareMutationalSignatureDataForTable(
         .map((mutationalSignatureSampleData, name) => ({
             name,
             samples: mutationalSignatureSampleData,
+            description: mutationalSignatureSampleData[0].meta.description,
             url: mutationalSignatureSampleData[0].meta.url,
         }))
         .value();
     for (const mutationalSignature of sampleInvertedDataByMutationalSignature) {
         let mutationalSignatureRowForTable: IMutationalSignatureRow = {
             name: '',
             sampleValues: {},
+            description: '',
             url: '',
         };
 
         mutationalSignatureRowForTable.name = mutationalSignature.name;
+        mutationalSignatureRowForTable.description =
+            mutationalSignature.description;
         mutationalSignatureRowForTable.url = mutationalSignature.url;
         if (
             Object.keys(mutationalSignature.samples).length ===