From ff177bd3c0858472924e02562fe6055fefc3dd9b Mon Sep 17 00:00:00 2001 From: "Abeshouse, Adam A./Sloan Kettering Institute" Date: Fri, 18 Oct 2019 14:18:21 -0400 Subject: [PATCH 1/4] Dont filter out profiles without data for selection in coexpression and plots tab Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute Former-commit-id: f83a3a3abe2c12fdfae5de60a8980b474748e4d1 --- src/pages/resultsView/ResultsViewPageStore.ts | 6 +++--- src/pages/resultsView/plots/PlotsTab.tsx | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/pages/resultsView/ResultsViewPageStore.ts b/src/pages/resultsView/ResultsViewPageStore.ts index 91f89606dea..10d526a7c7f 100644 --- a/src/pages/resultsView/ResultsViewPageStore.ts +++ b/src/pages/resultsView/ResultsViewPageStore.ts @@ -1243,15 +1243,15 @@ export class ResultsViewPageStore { }); readonly coexpressionTabMolecularProfiles = remoteData({ - await: () => [this.molecularProfilesWithData], + await: () => [this.molecularProfilesInStudies], invoke: () => Promise.resolve( sortRnaSeqProfilesToTop( filterAndSortProfiles( - this.molecularProfilesWithData.result! + this.molecularProfilesInStudies.result! ).concat( getGenesetProfiles( - this.molecularProfilesWithData.result! + this.molecularProfilesInStudies.result! ) ) ) diff --git a/src/pages/resultsView/plots/PlotsTab.tsx b/src/pages/resultsView/plots/PlotsTab.tsx index cbd06d00fa5..23fd4fc3b4f 100644 --- a/src/pages/resultsView/plots/PlotsTab.tsx +++ b/src/pages/resultsView/plots/PlotsTab.tsx @@ -977,11 +977,11 @@ export default class PlotsTab extends React.Component { readonly dataTypeToDataSourceOptions = remoteData<{[dataType:string]:{value:string, label:string}[]}>({ await:()=>[ - this.props.store.molecularProfilesWithData, + this.props.store.molecularProfilesInStudies, this.clinicalAttributeOptions ], invoke:()=>{ - const profiles = this.props.store.molecularProfilesWithData.result!; + const profiles = this.props.store.molecularProfilesInStudies.result!; const map = _.mapValues( _.groupBy(profiles, profile=>profile.molecularAlterationType), // create a map from profile type to list of profiles of that type profilesOfType=>( From 91eb5c923935bafcd56691167dd1e10c035e32cd Mon Sep 17 00:00:00 2001 From: "Abeshouse, Adam A./Sloan Kettering Institute" Date: Fri, 18 Oct 2019 15:18:20 -0400 Subject: [PATCH 2/4] Improve no-data message in coexpression tab Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute Former-commit-id: faf47c3b6b4ed6449f5ef99ec8605af964947331 --- .../coExpression/CoExpressionTab.tsx | 1 + .../coExpression/CoExpressionViz.tsx | 31 +++++++++++++------ 2 files changed, 22 insertions(+), 10 deletions(-) diff --git a/src/pages/resultsView/coExpression/CoExpressionTab.tsx b/src/pages/resultsView/coExpression/CoExpressionTab.tsx index e7785541b45..f8867865a45 100644 --- a/src/pages/resultsView/coExpression/CoExpressionTab.tsx +++ b/src/pages/resultsView/coExpression/CoExpressionTab.tsx @@ -279,6 +279,7 @@ export default class CoExpressionTab extends React.Component
-
- - {this.table} - -
-
- - {this.plot} - -
+ { this.dataStore.allData.length > 0 ? [ +
+ + {this.table} + +
, +
+ + {this.plot} + +
+ ] : ( +
+ There is no expression data for {this.props.geneticEntity.geneticEntityName} with the selected samples in {this.props.profileX.name}. +
+ )}
); From 00fa3ea8d0ca6279170a633497972a28263c3c8e Mon Sep 17 00:00:00 2001 From: "Abeshouse, Adam A./Sloan Kettering Institute" Date: Mon, 21 Oct 2019 19:04:12 -0400 Subject: [PATCH 3/4] Fix failing localdb test Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute Former-commit-id: 696c2f05ee8bf1a4930db21dee2c282ac1777ab3 --- end-to-end-test/local/specs/gsva.spec.js | 1 + 1 file changed, 1 insertion(+) diff --git a/end-to-end-test/local/specs/gsva.spec.js b/end-to-end-test/local/specs/gsva.spec.js index d802a8bae4f..62e400e8348 100644 --- a/end-to-end-test/local/specs/gsva.spec.js +++ b/end-to-end-test/local/specs/gsva.spec.js @@ -405,6 +405,7 @@ describe('gsva feature', function() { it('shows gene sets in table when GSVA scores selected in subject profile select box', () => { selectReactSelectOption($('.coexpression-select-query-profile'), 'GSVA scores on oncogenic signatures gene sets (5 samples)'); $('//*[@id="coexpressionTabGeneTabs"]').waitForExist(); + $('span*=GO_').waitForExist(); assert.equal($$('span*=GO_').length, 7); }); From 812c14f636340b7dbce52a37f20613bce1d278d2 Mon Sep 17 00:00:00 2001 From: "Abeshouse, Adam A./Sloan Kettering Institute" Date: Mon, 21 Oct 2019 19:20:46 -0400 Subject: [PATCH 4/4] Update API Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute Former-commit-id: 282fd6b9f1edcd52c019a9ecf2ed9c9716a013f0 --- src/shared/api/generated/CBioPortalAPIInternal-docs.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/shared/api/generated/CBioPortalAPIInternal-docs.json b/src/shared/api/generated/CBioPortalAPIInternal-docs.json index 4204704383d..de97aa630bf 100644 --- a/src/shared/api/generated/CBioPortalAPIInternal-docs.json +++ b/src/shared/api/generated/CBioPortalAPIInternal-docs.json @@ -1808,7 +1808,8 @@ "required": [ "counts", "entrezGeneId", - "hugoGeneSymbol" + "hugoGeneSymbol", + "pValue" ], "properties": { "counts": {