Merge pull request #3793 from Rajat-Sirohi/add-clinical-attributes-mu…

…tations-tab Add Clinical Attributes to Mutations Tab in Results View
cBioPortal · Jun 30, 2021 · ee9c19c · ee9c19c
2 parents 6b3dfd9 + c0be78f
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Showing 55 changed files with 724 additions and 55 deletions.
diff --git a/..._where_some_samples_have_ascn_data_and_some_do_not_element_chrome_1600x1000.png b/..._where_some_samples_have_ascn_data_and_some_do_not_element_chrome_1600x1000.png
diff --git a/...7_with_alk_and_sos1_-_sos1_should_be_not_sequenced_element_chrome_1600x1000.png b/...7_with_alk_and_sos1_-_sos1_should_be_not_sequenced_element_chrome_1600x1000.png
diff --git a/...sclc_tcga_broad_2016_for_query_egfr:_mut=t790m_amp_element_chrome_1600x1000.png b/...sclc_tcga_broad_2016_for_query_egfr:_mut=t790m_amp_element_chrome_1600x1000.png
diff --git a/...d_2016_with_cdkn2a_mdm2_and_merged_track_mdm4_tp53_element_chrome_1600x1000.png b/...d_2016_with_cdkn2a_mdm2_and_merged_track_mdm4_tp53_element_chrome_1600x1000.png
diff --git a/..._tab_-_nsclc_tcga_broad_2016_with_overlapping_tp53_element_chrome_1600x1000.png b/..._tab_-_nsclc_tcga_broad_2016_with_overlapping_tp53_element_chrome_1600x1000.png
diff --git a/...nce/download_tab_-_nsclc_tcga_broad_2016_with_tp53_element_chrome_1600x1000.png b/...nce/download_tab_-_nsclc_tcga_broad_2016_with_tp53_element_chrome_1600x1000.png
diff --git a/...cluding_unprofiled_samples_comparison_tab_clinical_element_chrome_1600x1000.png b/...cluding_unprofiled_samples_comparison_tab_clinical_element_chrome_1600x1000.png
diff --git a/...eference/excluding_unprofiled_samples_mutation_tab_element_chrome_1600x1000.png b/...eference/excluding_unprofiled_samples_mutation_tab_element_chrome_1600x1000.png
diff --git a/...s/reference/excluding_unprofiled_samples_mutex_tab_element_chrome_1600x1000.png b/...s/reference/excluding_unprofiled_samples_mutex_tab_element_chrome_1600x1000.png
diff --git a/...rison_page_microbiome_signature_tab_several_groups_element_chrome_1600x1000.png b/...rison_page_microbiome_signature_tab_several_groups_element_chrome_1600x1000.png
diff --git a/...omparison_page_microbiome_signature_tab_two_groups_element_chrome_1600x1000.png b/...omparison_page_microbiome_signature_tab_two_groups_element_chrome_1600x1000.png
diff --git a/...omparison_page_mrna_enrichments_tab_several_groups_element_chrome_1600x1000.png b/...omparison_page_mrna_enrichments_tab_several_groups_element_chrome_1600x1000.png
diff --git a/...up_comparison_page_mrna_enrichments_tab_two_groups_element_chrome_1600x1000.png b/...up_comparison_page_mrna_enrichments_tab_two_groups_element_chrome_1600x1000.png
diff --git a/...nce/no_session_comparison_tab_mutation_enrichments_element_chrome_1600x1000.png b/...nce/no_session_comparison_tab_mutation_enrichments_element_chrome_1600x1000.png
diff --git a/...mote/screenshots/reference/no_session_mutation_tab_element_chrome_1600x1000.png b/...mote/screenshots/reference/no_session_mutation_tab_element_chrome_1600x1000.png
diff --git a/.../remote/screenshots/reference/no_session_mutex_tab_element_chrome_1600x1000.png b/.../remote/screenshots/reference/no_session_mutex_tab_element_chrome_1600x1000.png
diff --git a/...reenshots/reference/patient_view_lgg_ucsf_2014_p04_element_chrome_1600x1000.png b/...reenshots/reference/patient_view_lgg_ucsf_2014_p04_element_chrome_1600x1000.png
diff --git a/...with_0_mutations_msk_impact_2017_p-0000053-t01-im3_element_chrome_1600x1000.png b/...with_0_mutations_msk_impact_2017_p-0000053-t01-im3_element_chrome_1600x1000.png
diff --git a/...ge_heatmap_with_two_mutations_selected_from_before_element_chrome_1600x1000.png b/...ge_heatmap_with_two_mutations_selected_from_before_element_chrome_1600x1000.png
diff --git a/...shots/reference/pvge_hover_a_mutation_with_heatmap_element_chrome_1600x1000.png b/...shots/reference/pvge_hover_a_mutation_with_heatmap_element_chrome_1600x1000.png
diff --git a/...nshots/reference/pvge_initial_view_with_line_chart_element_chrome_1600x1000.png b/...nshots/reference/pvge_initial_view_with_line_chart_element_chrome_1600x1000.png
diff --git a/.../reference/pvge_one_mutation_selected_with_heatmap_element_chrome_1600x1000.png b/.../reference/pvge_one_mutation_selected_with_heatmap_element_chrome_1600x1000.png
diff --git a/...ference/pvge_one_mutation_selected_with_line_chart_element_chrome_1600x1000.png b/...ference/pvge_one_mutation_selected_with_line_chart_element_chrome_1600x1000.png
diff --git a/...st/remote/screenshots/reference/pvge_show_timeline_element_chrome_1600x1000.png b/...st/remote/screenshots/reference/pvge_show_timeline_element_chrome_1600x1000.png
diff --git a/...arison_tab_clinical_tab_bar_chart_chi_squared_test_element_chrome_1600x1000.png b/...arison_tab_clinical_tab_bar_chart_chi_squared_test_element_chrome_1600x1000.png
diff --git a/...on_tab_clinical_tab_log_scale__kruskal_wallis_test_element_chrome_1600x1000.png b/...on_tab_clinical_tab_log_scale__kruskal_wallis_test_element_chrome_1600x1000.png
diff --git a/...chart_exclude_overlapping_samples_chi_squared_test_element_chrome_1600x1000.png b/...chart_exclude_overlapping_samples_chi_squared_test_element_chrome_1600x1000.png
diff --git a/...ab_clinical_tab_stacked_bar_chart_chi_squared_test_element_chrome_1600x1000.png b/...ab_clinical_tab_stacked_bar_chart_chi_squared_test_element_chrome_1600x1000.png
diff --git a/...stacked_bar_chart_horizontal_bars_chi_squared_test_element_chrome_1600x1000.png b/...stacked_bar_chart_horizontal_bars_chi_squared_test_element_chrome_1600x1000.png
diff --git a/...tab_stacked_bar_chart_swaped_axes_chi_squared_test_element_chrome_1600x1000.png b/...tab_stacked_bar_chart_swaped_axes_chi_squared_test_element_chrome_1600x1000.png
diff --git a/...n_tab_clinical_tab_swaped_axes_kruskal_wallis_test_element_chrome_1600x1000.png b/...n_tab_clinical_tab_swaped_axes_kruskal_wallis_test_element_chrome_1600x1000.png
diff --git a/..._comparison_tab_protein_enrichments_tab_two_groups_element_chrome_1600x1000.png b/..._comparison_tab_protein_enrichments_tab_two_groups_element_chrome_1600x1000.png
diff --git a/...erence/session_comparison_tab_mutation_enrichments_element_chrome_1600x1000.png b/...erence/session_comparison_tab_mutation_enrichments_element_chrome_1600x1000.png
diff --git a/.../remote/screenshots/reference/session_mutation_tab_element_chrome_1600x1000.png b/.../remote/screenshots/reference/session_mutation_tab_element_chrome_1600x1000.png
diff --git a/...est/remote/screenshots/reference/session_mutex_tab_element_chrome_1600x1000.png b/...est/remote/screenshots/reference/session_mutex_tab_element_chrome_1600x1000.png
diff --git a/..._adding_charts,_each_chart_should_get_proper_data._element_chrome_1600x1000.png b/..._adding_charts,_each_chart_should_get_proper_data._element_chrome_1600x1000.png
diff --git a/end-to-end-test/remote/specs/core/mutationTable.spec.js b/end-to-end-test/remote/specs/core/mutationTable.spec.js
@@ -36,8 +36,12 @@ describe('Mutation Table', function() {
 
             // click on column button
             browser.click('button*=Columns');
-            // scroll down to activated "exon" selection
-            browser.scroll(1000, 1000);
+            // scroll down to activated "Exon" selection
+            browser.execute(
+                'document.getElementsByClassName("ReactVirtualized__Grid")[0].scroll(1000, 1000)'
+            );
+            // wait for exon checkbox to appear
+            browser.pause(2000);
             // click "exon"
             browser.click('//*[text()="Exon"]');
             // check if three exact matches for 6 appear
@@ -114,13 +118,15 @@ describe('Mutation Table', function() {
                 60000
             );
             // show the gnomad column
-            browser.scroll(1000, 0);
+            browser.scroll(0, 1000);
             // click on column button
             browser.click('button*=Columns');
             // scroll down to activated "GNOMAD" selection
-            browser.scroll(1000, 1000);
-            // wait for gnomad checkbox appear
-            browser.waitForVisible('[data-id=gnomAD]', 60000);
+            browser.execute(
+                'document.getElementsByClassName("ReactVirtualized__Grid")[0].scroll(1000, 1000)'
+            );
+            // wait for gnomad checkbox to appear
+            browser.pause(2000);
             // click "GNOMAD"
             browser.click('//*[text()="gnomAD"]');
             // find frequency
@@ -172,7 +178,11 @@ describe('Mutation Table', function() {
             // click on column button
             browser.click('button*=Columns');
             // scroll down to activated "ClinVar" selection
-            browser.scroll(1000, 1000);
+            browser.execute(
+                'document.getElementsByClassName("ReactVirtualized__Grid")[0].scroll(1000, 1000)'
+            );
+            // wait for clinvar checkbox to appear
+            browser.pause(2000);
             // click "clinvar"
             browser.click('//*[text()="ClinVar"]');
             let res;
@@ -206,7 +216,11 @@ describe('Mutation Table', function() {
             // click on column button
             browser.click('button*=Columns');
             // scroll down to activated "dbSNP" selection
-            browser.scroll(1000, 1000);
+            browser.execute(
+                'document.getElementsByClassName("ReactVirtualized__Grid")[0].scroll(1000, 1000)'
+            );
+            // wait for dbSNP checkbox to appear
+            browser.pause(2000);
             // click "dbSNP"
             browser.click('//*[text()="dbSNP"]');
             let res;

diff --git a/src/pages/resultsView/ResultsViewPageStore.ts b/src/pages/resultsView/ResultsViewPageStore.ts
@@ -69,6 +69,7 @@ import GenomeNexusCache from 'shared/cache/GenomeNexusCache';
 import GenomeNexusMutationAssessorCache from 'shared/cache/GenomeNexusMutationAssessorCache';
 import CancerTypeCache from 'shared/cache/CancerTypeCache';
 import MutationCountCache from 'shared/cache/MutationCountCache';
+import ClinicalAttributeCache from 'shared/cache/ClinicalAttributeCache';
 import DiscreteCNACache from 'shared/cache/DiscreteCNACache';
 import PdbHeaderCache from 'shared/cache/PdbHeaderCache';
 import {
@@ -1143,6 +1144,26 @@ export class ResultsViewPageStore {
         },
     });
 
+    // TODO: Should include all clinical attributes, not just server attributes
+    readonly mutationsTabClinicalAttributes = remoteData<ClinicalAttribute[]>({
+        await: () => [this.studyIds],
+        invoke: async () => {
+            const clinicalAttributes = await client.fetchClinicalAttributesUsingPOST(
+                {
+                    studyIds: this.studyIds.result!,
+                }
+            );
+            const excludeList = ['CANCER_TYPE_DETAILED', 'MUTATION_COUNT'];
+
+            return _.uniqBy(
+                clinicalAttributes.filter(
+                    x => !excludeList.includes(x.clinicalAttributeId)
+                ),
+                x => x.clinicalAttributeId
+            );
+        },
+    });
+
     readonly clinicalAttributeIdToClinicalAttribute = remoteData({
         await: () => [this.clinicalAttributes],
         invoke: () =>
@@ -1255,6 +1276,22 @@ export class ResultsViewPageStore {
         },
     });
 
+    readonly clinicalAttributeIdToAvailableFrequency = remoteData({
+        await: () => [
+            this.clinicalAttributeIdToAvailableSampleCount,
+            this.samples,
+        ],
+        invoke: () => {
+            const numSamples = this.samples.result!.length;
+            return Promise.resolve(
+                _.mapValues(
+                    this.clinicalAttributeIdToAvailableSampleCount.result!,
+                    count => (100 * count) / numSamples
+                )
+            );
+        },
+    });
+
     readonly cnSegments = remoteData<CopyNumberSeg[]>(
         {
             await: () => [this.filteredSamples],
@@ -3428,6 +3465,7 @@ export class ResultsViewPageStore {
             this.oncoKbCancerGenes,
             () => this.mutationsByGene.result![gene.hugoGeneSymbol] || [],
             () => this.mutationCountCache,
+            () => this.clinicalAttributeCache,
             () => this.genomeNexusCache,
             () => this.genomeNexusMutationAssessorCache,
             () => this.discreteCNACache,
@@ -3442,6 +3480,8 @@ export class ResultsViewPageStore {
             this.uniqueSampleKeyToTumorType.result!,
             this.generateGenomeNexusHgvsgUrl,
             this.clinicalDataGroupedBySampleMap,
+            this.mutationsTabClinicalAttributes,
+            this.clinicalAttributeIdToAvailableFrequency,
             this.genomeNexusClient,
             this.genomeNexusInternalClient,
             () => this.urlWrapper.query.mutations_transcript_id
@@ -5325,6 +5365,10 @@ export class ResultsViewPageStore {
         return new MutationCountCache();
     }
 
+    @cached @computed get clinicalAttributeCache() {
+        return new ClinicalAttributeCache();
+    }
+
     @cached @computed get pdbHeaderCache() {
         return new PdbHeaderCache();
     }