From f0f3455ab450f7b258e3c69fe84dc985e23c80f6 Mon Sep 17 00:00:00 2001 From: "Abeshouse, Adam A./Sloan Kettering Institute" Date: Mon, 27 Jan 2020 17:13:44 -0500 Subject: [PATCH] Run prettier on all files Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute Former-commit-id: 9c89f21b55bc37e169bf5f92ea93af50ad19c1bd --- src/AppStore.ts | 86 +- src/appBootstrapper.jsx | 80 +- src/appShell/App/Container.tsx | 86 +- src/appShell/App/PortalFooter.tsx | 306 +- src/appShell/App/PortalHeader.tsx | 254 +- src/appShell/App/footer.scss | 8 +- src/appShell/DevTools/DevTools.js | 14 +- src/config/IAppConfig.ts | 2 +- src/config/config.spec.ts | 40 +- src/config/config.ts | 169 +- src/config/test.config.ts | 6 +- src/global.spec.ts | 45 +- src/globalStyles/bootstrap-entry.scss | 6 +- src/globalStyles/custom-icons.scss | 22 +- src/globalStyles/e2etest.scss | 42 +- src/globalStyles/global.scss | 803 ++- src/globalStyles/header.scss | 194 +- src/globalStyles/legacy-template.scss | 35 +- src/globalStyles/legacy.scss | 21 +- src/globalStyles/prefixed-global.scss | 12 +- src/globalStyles/variables.scss | 38 +- src/pages/groupComparison/ClinicalData.tsx | 600 +- .../ClinicalDataEnrichmentsTable.tsx | 133 +- .../groupComparison/CopyNumberEnrichments.tsx | 112 +- .../CreateGroupFromOverlap.tsx | 205 +- .../GroupComparisonLoading.tsx | 98 +- .../groupComparison/GroupComparisonPage.tsx | 320 +- .../groupComparison/GroupComparisonStore.ts | 1479 +++-- .../groupComparison/GroupComparisonTabs.ts | 16 +- .../GroupComparisonURLWrapper.ts | 32 +- .../GroupComparisonUtils.spec.ts | 4104 +++++++++----- .../groupComparison/GroupComparisonUtils.tsx | 700 ++- src/pages/groupComparison/MRNAEnrichments.tsx | 95 +- .../groupComparison/MutationEnrichments.tsx | 115 +- src/pages/groupComparison/Overlap.tsx | 352 +- .../OverlapExclusionIndicator.tsx | 157 +- src/pages/groupComparison/OverlapUpset.tsx | 165 +- .../groupComparison/OverlapUtils.spec.tsx | 788 +-- 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.../normalizeLayout.spec.ts | 98 +- .../rectangleVennDiagram/normalizeLayout.ts | 117 +- src/pages/groupComparison/styles.module.scss | 70 +- src/pages/home/HomePage.tsx | 80 +- src/pages/home/homePage.scss | 2 +- .../PatientViewGenePanelModal/GenesList.tsx | 54 +- .../styles.module.scss | 32 +- .../patientView/PatientViewPage.spec.tsx | 28 +- src/pages/patientView/PatientViewPage.tsx | 1632 ++++-- src/pages/patientView/PatientViewPageTabs.ts | 18 +- .../patientView/PatientViewPageUtils.spec.tsx | 35 +- .../patientView/PatientViewPageUtils.tsx | 25 +- .../patientView/PatientViewUrlWrapper.ts | 12 +- src/pages/patientView/SVGIcons.tsx | 50 +- src/pages/patientView/SampleManager.tsx | 284 +- ...formationMutationalSignatureTable.spec.tsx | 74 +- ...calInformationMutationalSignatureTable.tsx | 186 +- .../ClinicalInformationPatientTable.spec.tsx | 14 +- .../ClinicalInformationPatientTable.tsx | 156 +- .../ClinicalInformationSamplesTable.spec.tsx | 14 +- 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.../mutation/VAFLineChartUtils.spec.ts | 996 ++-- .../patientView/mutation/VAFLineChartUtils.ts | 125 +- .../column/AlleleFreqColumnFormatter.spec.tsx | 95 +- .../column/AlleleFreqColumnFormatter.tsx | 222 +- .../column/TumorColumnFormatter.spec.tsx | 100 +- .../mutation/column/TumorColumnFormatter.tsx | 251 +- .../mutation/oncoprint/MutationOncoprint.tsx | 496 +- .../oncoprint/MutationOncoprintUtils.spec.ts | 1544 +++-- .../oncoprint/MutationOncoprintUtils.ts | 154 +- .../mutation/oncoprint/styles.module.scss | 73 +- src/pages/patientView/mutation/style.scss | 2 +- .../patientView/mutation/styles.module.scss | 20 +- .../pathologyReport/PathologyReport.tsx | 84 +- src/pages/patientView/patient.scss | 110 +- .../ClinicalAttributesInline.spec.tsx | 14 +- .../ClinicalAttributesInline.tsx | 4 +- .../patientHeader/PatientHeader.spec.tsx | 14 +- .../patientHeader/PatientHeader.tsx | 126 +- .../patientHeader/SampleInline.spec.tsx | 94 +- .../patientHeader/SampleInline.tsx | 71 +- 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+- .../mutation/ResultsViewMutationTable.tsx | 87 +- src/pages/resultsView/mutation/mutations.scss | 9 +- .../resultsView/mutationCountHelpers.spec.ts | 211 +- src/pages/resultsView/mutationCountHelpers.ts | 23 +- .../MutualExclusivityTab.tsx | 141 +- .../MutualExclusivityTable.tsx | 198 +- .../MutualExclusivityUtil.spec.tsx | 550 +- .../MutualExclusivityUtil.tsx | 212 +- .../mutualExclusivity/styles.module.scss | 18 +- .../oncoprint/AddClinicalTracks.tsx | 251 +- .../oncoprint/OncoprintDropdownCount.tsx | 15 +- .../LastPlotsTabSelectionForDatatype.spec.ts | 178 +- .../plots/LastPlotsTabSelectionForDatatype.ts | 95 +- src/pages/resultsView/plots/PlotsTab.spec.tsx | 42 +- src/pages/resultsView/plots/PlotsTab.tsx | 2718 ++++++--- .../resultsView/plots/PlotsTabUtils.spec.ts | 913 +-- src/pages/resultsView/plots/PlotsTabUtils.tsx | 2435 +++++--- .../resultsView/plots/QuickPlots.spec.ts | 584 +- src/pages/resultsView/plots/QuickPlots.ts | 357 +- src/pages/resultsView/plots/styles.scss | 267 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src/shared/components/ValidationAlert.tsx | 15 +- .../WindowWidthBox/WindowWidthBox.tsx | 42 +- .../components/annotation/Civic.spec.tsx | 133 +- src/shared/components/annotation/Civic.tsx | 103 +- .../components/annotation/CivicCard.spec.tsx | 30 +- .../components/annotation/CivicCard.tsx | 74 +- .../annotation/MyCancerGenome.spec.tsx | 49 +- .../components/annotation/MyCancerGenome.tsx | 81 +- .../genomeNexus/MutationAssessor.tsx | 129 +- .../annotation/genomeNexus/PolyPhen2.tsx | 78 +- .../annotation/genomeNexus/Sift.tsx | 65 +- .../styles/mutationAssessorColumn.module.scss | 18 +- .../mutationAssessorTooltip.module.scss | 34 +- .../styles/polyPhen2Tooltip.module.scss | 22 +- .../styles/siftTooltip.module.scss | 20 +- .../annotation/styles/annotation.module.scss | 26 +- .../annotation/styles/civicCard.scss | 59 +- .../styles/myCancerGenome.module.scss | 6 +- .../banners/AlterationFilterWarning.tsx | 209 +- src/shared/components/banners/InfoBanner.tsx | 27 +- .../components/banners/OqlStatusBanner.tsx | 95 +- src/shared/components/banners/styles.scss | 14 +- src/shared/components/barGraph/BarGraph.tsx | 231 +- .../cnSegments/CNSegmentsDownloader.tsx | 64 +- .../components/cohort/FrequencyBar.spec.tsx | 111 +- src/shared/components/cohort/FrequencyBar.tsx | 64 +- src/shared/components/cohort/LetterIcon.tsx | 41 +- .../ColumnVisibilityControls.spec.tsx | 48 +- .../ColumnVisibilityControls.tsx | 87 +- .../CopyDownloadButtons.tsx | 46 +- .../CopyDownloadControls.spec.tsx | 129 +- .../CopyDownloadControls.tsx | 167 +- .../CopyDownloadLinks.tsx | 64 +- .../CopyDownloadQueryLinks.tsx | 132 +- .../ICopyDownloadControls.ts | 7 +- .../SimpleCopyDownloadControls.tsx | 77 +- .../copyDownloadControls.module.scss | 4 +- .../cosmic/CosmicMutationTable.spec.tsx | 14 +- .../components/cosmic/CosmicMutationTable.tsx | 73 +- .../DataAccessTokensDropdown.tsx | 86 +- .../EnhancedFixedDataTable.jsx | 1168 ++-- .../enhancedFixedDataTable/styles.css | 24 +- .../enhancedFixedDataTable/styles.module.scss | 31 +- .../EnhancedReactTable.spec.tsx | 14 +- .../enhancedReactTable/EnhancedReactTable.tsx | 522 +- .../IColumnFormatter.spec.tsx | 14 +- .../enhancedReactTable/IColumnFormatter.ts | 22 +- .../IEnhancedReactTableProps.spec.tsx | 14 +- .../IEnhancedReactTableProps.ts | 31 +- .../components/enhancedReactTable/styles.css | 2 +- src/shared/components/errorBox/ErrorBox.tsx | 49 +- .../components/errorBox/styles.module.scss | 26 +- .../components/errorScreen/ErrorScreen.tsx | 115 +- .../components/errorScreen/errorScreen.scss | 57 +- .../featureTitle/FeatureTitle.spec.tsx | 10 +- .../components/featureTitle/FeatureTitle.tsx | 43 +- src/shared/components/flexbox/FlexBox.tsx | 67 +- .../components/flexbox/styles.module.scss | 24 +- .../components/iframeLoader/IFrameLoader.tsx | 51 +- .../igv/IntegrativeGenomicsViewer.tsx | 120 +- .../components/infoBeacon/InfoBeacon.tsx | 63 +- .../components/infoBeacon/styles.module.scss | 48 +- .../labeledCheckbox/LabeledCheckbox.tsx | 99 +- .../labeledCheckbox/styles.module.scss | 24 +- .../lazyMobXTable/LazyMobXTable.spec.tsx | 3132 +++++++--- .../lazyMobXTable/LazyMobXTable.tsx | 883 +-- .../components/lazyMobXTable/styles.scss | 36 +- src/shared/components/lazyMobXTable/utils.ts | 8 +- .../LoadingIndicator.spec.tsx | 12 +- .../loadingIndicator/LoadingIndicator.tsx | 91 +- .../loadingIndicator/styles.module.scss | 110 +- .../miniOncoprint/MiniOncoprint.tsx | 100 +- .../miniOncoprint/styles.module.scss | 53 +- .../mutationMapper/MutationMapper.tsx | 210 +- .../mutationMapper/MutationMapperConfig.ts | 12 +- .../MutationMapperDataStore.spec.ts | 282 +- .../mutationMapper/MutationMapperDataStore.ts | 174 +- .../mutationMapper/MutationMapperStore.ts | 275 +- .../MutationMapperUserSelectionStore.ts | 10 +- .../mutationMapper/MutationMapperUtils.ts | 12 +- .../mutationMapper/PdbChainDataStore.ts | 33 +- .../mutationMapper/mutationMapper.module.scss | 10 +- .../mutationTable/MutationTable.tsx | 1079 ++-- .../AlleleCountColumnFormatter.spec.tsx | 67 +- .../column/AlleleCountColumnFormatter.tsx | 79 +- .../column/AnnotationColumnFormatter.spec.tsx | 34 +- .../column/AnnotationColumnFormatter.tsx | 435 +- .../column/CancerTypeColumnFormatter.tsx | 95 +- .../CancerTypeColumnFormatterLazyLoaded.tsx | 97 +- .../column/ChromosomeColumnFormatter.spec.tsx | 46 +- .../column/ChromosomeColumnFormatter.tsx | 32 +- .../column/ClinVarColumnFormatter.tsx | 120 +- .../column/CohortColumnFormatter.spec.tsx | 14 +- .../column/CohortColumnFormatter.tsx | 190 +- .../column/CosmicColumnFormatter.spec.tsx | 142 +- .../column/CosmicColumnFormatter.tsx | 127 +- .../column/DbsnpColumnFormatter.tsx | 140 +- .../column/DiscreteCNAColumnFormatter.tsx | 268 +- .../column/ExonColumnFormatter.tsx | 160 +- .../FunctionalImpactColumnFormatter.tsx | 429 +- .../column/GeneColumnFormatter.spec.tsx | 22 +- .../column/GeneColumnFormatter.tsx | 25 +- .../column/GnomadColumnFormatter.tsx | 154 +- .../column/HgvscColumnFormatter.tsx | 128 +- .../column/HgvsgColumnFormatter.tsx | 61 +- .../column/MrnaExprColumnFormatter.spec.tsx | 14 +- .../column/MrnaExprColumnFormatter.tsx | 192 +- .../column/MutationCountColumnFormatter.tsx | 62 +- .../MutationStatusColumnFormatter.spec.tsx | 90 +- .../column/MutationStatusColumnFormatter.tsx | 46 +- .../MutationTypeColumnFormatter.spec.tsx | 141 +- .../column/MutationTypeColumnFormatter.tsx | 255 +- .../NormalAlleleFreqColumnFormatter.tsx | 48 +- .../column/PanelColumnFormatter.spec.tsx | 109 +- .../column/PanelColumnFormatter.tsx | 182 +- .../ProteinChangeColumnFormatter.spec.tsx | 119 +- .../column/ProteinChangeColumnFormatter.tsx | 69 +- .../column/SampleColumnFormatter.spec.tsx | 50 +- .../column/SampleColumnFormatter.tsx | 42 +- .../column/StudyColumnFormatter.tsx | 87 +- .../column/TumorAlleleFreqColumnFormatter.tsx | 54 +- .../ValidationStatusColumnFormatter.spec.tsx | 122 +- .../ValidationStatusColumnFormatter.tsx | 73 +- .../mutationTable/column/cosmic.module.scss | 6 +- .../mutationTable/column/exon.module.scss | 2 +- .../mutationTable/column/hgvsg.module.scss | 27 +- .../column/mutationAssessor.module.scss | 50 +- .../column/mutationStatus.module.scss | 28 +- .../column/mutationType.module.scss | 22 +- .../column/proteinChange.module.scss | 12 +- .../mutationTable/column/styles.module.scss | 8 +- .../column/validationStatus.module.scss | 30 +- .../components/oncoprint/DataUtils.spec.ts | 3317 ++++++----- src/shared/components/oncoprint/DataUtils.ts | 569 +- .../components/oncoprint/DeltaUtils.spec.ts | 1001 +++- src/shared/components/oncoprint/DeltaUtils.ts | 1144 ++-- src/shared/components/oncoprint/Oncoprint.tsx | 318 +- .../oncoprint/OncoprintUtils.spec.ts | 519 +- .../components/oncoprint/OncoprintUtils.ts | 1137 ++-- .../oncoprint/ResultsViewOncoprint.spec.tsx | 145 +- .../oncoprint/ResultsViewOncoprint.tsx | 1403 +++-- .../ResultsViewOncoprintUtils.spec.ts | 509 +- .../oncoprint/ResultsViewOncoprintUtils.tsx | 305 +- .../components/oncoprint/SortUtils.spec.ts | 448 +- src/shared/components/oncoprint/SortUtils.ts | 174 +- .../components/oncoprint/TooltipUtils.spec.ts | 3047 +++++++--- .../components/oncoprint/TooltipUtils.ts | 865 ++- .../oncoprint/controls/ConfirmNgchmModal.tsx | 51 +- .../oncoprint/controls/CustomDropdown.tsx | 61 +- .../oncoprint/controls/NonClosingDropdown.tsx | 50 +- .../oncoprint/controls/OncoprintControls.tsx | 207 +- .../components/oncoprint/controls/styles.scss | 301 +- .../components/oncoprint/geneticrules.ts | 672 ++- src/shared/components/oncoprint/styles.scss | 60 +- .../components/oncoprint/tabularDownload.ts | 200 +- .../OverlappingStudiesWarning.tsx | 20 +- .../components/pageNotFound/PageNotFound.tsx | 6 +- .../PaginationControls.spec.tsx | 82 +- .../paginationControls/PaginationControls.tsx | 357 +- .../paginationControls.module.scss | 4 +- .../components/plots/BoxScatterPlot.tsx | 721 ++- .../plots/MultipleCategoryBarPlot.tsx | 587 +- .../MultipleCategoryBarPlotUtils.spec.ts | 3714 ++++++++---- .../plots/MultipleCategoryBarPlotUtils.ts | 167 +- src/shared/components/plots/PlotUtils.spec.ts | 40 +- src/shared/components/plots/PlotUtils.ts | 334 +- src/shared/components/plots/ScatterPlot.tsx | 419 +- .../components/plots/ScatterPlotTooltip.tsx | 62 +- .../components/plots/ScatterPlotUtils.spec.ts | 93 +- .../components/plots/ScatterPlotUtils.ts | 14 +- src/shared/components/plots/TablePlot.tsx | 310 +- src/shared/components/plots/TablePlotUtils.ts | 59 +- src/shared/components/plots/TickUtils.ts | 54 +- .../components/plots/WaterfallPlot.spec.tsx | 91 +- src/shared/components/plots/WaterfallPlot.tsx | 609 +- .../components/plots/WaterfallPlotTooltip.tsx | 55 +- .../plots/downsampleByGrouping.spec.ts | 140 +- .../components/plots/downsampleByGrouping.ts | 90 +- .../progressIndicator/ProgressIndicator.tsx | 116 +- .../progressIndicator/styles.module.scss | 74 +- .../proteinChainPanel/PdbChainTable.tsx | 183 +- .../proteinChainPanel/ProteinChain.tsx | 74 +- .../proteinChainPanel/ProteinChainPanel.tsx | 283 +- .../proteinChainPanel/ProteinChainView.tsx | 123 +- .../column/OrganismColumnFormatter.tsx | 43 +- .../components/query/CancerStudySelector.tsx | 440 +- .../components/query/CancerStudyTreeData.ts | 460 +- .../components/query/CaseSetSelector.spec.tsx | 28 +- .../components/query/CaseSetSelector.tsx | 304 +- .../query/CaseSetSelectorUtils.spec.ts | 169 +- .../components/query/CaseSetSelectorUtils.ts | 131 +- .../query/DataTypePrioritySelector.spec.tsx | 54 +- .../query/DataTypePrioritySelector.tsx | 168 +- .../components/query/GeneSetSelector.tsx | 4 +- .../query/GenesetsHierarchyFilterForm.tsx | 106 +- .../query/GenesetsHierarchySelector.tsx | 111 +- .../components/query/GenesetsJsTree.tsx | 348 +- .../query/GenesetsSelectorStore.spec.ts | 173 +- .../query/GenesetsSelectorStore.tsx | 47 +- .../query/GenesetsVolcanoSelector.tsx | 507 +- .../components/query/GisticGeneSelector.tsx | 442 +- .../query/MolecularProfileSelector.tsx | 367 +- .../components/query/MutSigGeneSelector.tsx | 285 +- .../query/QueryAndDownloadTab.spec.tsx | 18 +- .../components/query/QueryAndDownloadTabs.tsx | 120 +- .../components/query/QueryContainer.tsx | 526 +- .../components/query/QueryStore.spec.ts | 123 +- src/shared/components/query/QueryStore.ts | 41 +- .../components/query/QueryStoreUtils.spec.ts | 448 +- .../components/query/QueryStoreUtils.ts | 304 +- .../components/query/QuickSelectButtons.tsx | 81 +- src/shared/components/query/StudyListLogic.ts | 314 +- .../components/query/StudySelectorStats.tsx | 91 +- src/shared/components/query/gene_lists.ts | 584 +- .../query/quickSearch/HomePageSummary.tsx | 25 +- .../query/quickSearch/QuickSearch.tsx | 4 +- .../query/quickSearch/styles.module.scss | 50 +- .../components/query/quickSearch/styles.scss | 7 +- .../components/query/studyList/StudyList.tsx | 318 +- .../query/studyList/styles.module.scss | 394 +- .../components/query/styles/jstree/style.css | 1259 ++-- .../components/query/styles/queryModal.scss | 4 +- .../query/styles/styles.module.scss | 2 +- src/shared/components/rightbar/RightBar.tsx | 296 +- .../sampleLabel/SampleLabel.spec.tsx | 14 +- .../components/sampleLabel/SampleLabel.tsx | 48 +- .../sampleLabel/SampleLabelNotProfiled.tsx | 39 +- .../sectionHeader/SectionHeader.tsx | 92 +- .../sectionHeader/styles.module.scss | 28 +- .../simpleTable/SimpleTable.spec.tsx | 74 +- .../components/simpleTable/SimpleTable.tsx | 54 +- src/shared/components/simpleTable/styles.scss | 78 +- .../staticContent/StaticContent.tsx | 75 +- src/shared/components/staticContent/gfm.css | 275 +- .../structureViewer/PdbResidueUtils.spec.ts | 161 +- .../structureViewer/PdbResidueUtils.ts | 60 +- .../PyMolScriptGenerator.spec.ts | 403 +- .../structureViewer/PyMolScriptGenerator.ts | 221 +- .../structureViewer/StructureViewer.tsx | 59 +- .../structureViewer/StructureViewerPanel.tsx | 670 ++- .../structureViewer/StructureVisualizer.ts | 154 +- .../StructureVisualizer3D.spec.ts | 648 ++- .../structureViewer/StructureVisualizer3D.ts | 427 +- .../structureViewer.module.scss | 82 +- .../studyTagsTooltip/StudyTagsTooltip.scss | 51 +- .../studyTagsTooltip/StudyTagsTooltip.tsx | 92 +- .../TableHeaderControls.spec.tsx | 99 +- .../TableHeaderControls.tsx | 183 +- .../components/testimonials/Testimonials.tsx | 45 +- .../testimonials/testimonials.module.scss | 16 +- .../components/textIconArea/TextIconArea.tsx | 105 +- .../unknownStudies/UnknownStudiesWarning.tsx | 26 +- .../UnsupportedBrowserModal.spec.tsx | 10 +- .../UnsupportedBrowserModal.tsx | 82 +- .../components/userMessager/UserMessage.tsx | 74 +- .../userMessager/styles.module.scss | 23 +- src/shared/components/window/WindowStore.ts | 4 +- .../components/wrappedTour/WrappedTour.tsx | 44 +- src/shared/enums/ErrorEnums.ts | 6 +- src/shared/lib/AnnotationUtils.spec.tsx | 208 +- src/shared/lib/AnnotationUtils.ts | 61 +- src/shared/lib/ArrayUtils.spec.ts | 28 +- src/shared/lib/ArrayUtils.ts | 8 +- src/shared/lib/CBioPortalAPIUtils.ts | 22 +- src/shared/lib/CancerHotspotsUtils.spec.ts | 25 +- src/shared/lib/CancerHotspotsUtils.ts | 41 +- src/shared/lib/CivicUtils.ts | 142 +- src/shared/lib/Colors.ts | 47 +- src/shared/lib/ContextUtils.ts | 56 +- src/shared/lib/CopyNumberUtils.ts | 5 +- src/shared/lib/EventUtils.ts | 7 +- src/shared/lib/ExtendedRouterStore.spec.ts | 131 +- src/shared/lib/ExtendedRouterStore.ts | 70 +- src/shared/lib/FilenameUtils.spec.ts | 64 +- src/shared/lib/FilenameUtils.ts | 16 +- src/shared/lib/FisherExactTestCalculator.ts | 37 +- src/shared/lib/FormatUtils.spec.tsx | 146 +- src/shared/lib/FormatUtils.tsx | 74 +- .../GenericAssayCommonUtils.ts | 2 +- .../lib/GenericAssayUtils/TreatmentUtils.ts | 197 +- src/shared/lib/GisticUtils.ts | 53 +- src/shared/lib/HotspotSet.spec.ts | 249 +- src/shared/lib/HotspotSet.ts | 44 +- src/shared/lib/IGVUtils.spec.ts | 523 +- src/shared/lib/IGVUtils.ts | 100 +- ...ILazyMobXTableApplicationDataStore.spec.ts | 163 +- .../lib/ILazyMobXTableApplicationDataStore.ts | 124 +- ...TableApplicationLazyDownloadDataFetcher.ts | 2 +- src/shared/lib/ISortMetric.ts | 6 +- src/shared/lib/LazyLoadedTableCell.tsx | 37 +- src/shared/lib/LazyMemo.spec.ts | 153 +- src/shared/lib/LazyMemo.ts | 14 +- src/shared/lib/LazyMobXCache.spec.ts | 701 ++- src/shared/lib/LazyMobXCache.ts | 206 +- src/shared/lib/ListIndexedMap.spec.ts | 204 +- src/shared/lib/ListIndexedMap.ts | 57 +- src/shared/lib/LogicUtils.spec.ts | 25 +- src/shared/lib/LogicUtils.ts | 17 +- src/shared/lib/MDACCUtils.spec.ts | 10 +- src/shared/lib/MDACCUtils.ts | 4 +- src/shared/lib/MemoizedHandlerFactory.ts | 20 +- src/shared/lib/MobxPromiseCache.ts | 53 +- src/shared/lib/MutationInputParser.spec.ts | 750 ++- src/shared/lib/MutationInputParser.ts | 216 +- .../lib/MutationTableDownloadDataFetcher.ts | 176 +- src/shared/lib/MutationUtils.spec.ts | 766 ++- src/shared/lib/MutationUtils.ts | 295 +- src/shared/lib/MutationalSignaturesUtils.tsx | 127 +- src/shared/lib/NumberUtils.ts | 9 +- src/shared/lib/ObjectManipulation.spec.ts | 35 +- src/shared/lib/ObjectManipulation.ts | 44 +- src/shared/lib/OncoKbUtils.ts | 134 +- src/shared/lib/PdbUtils.spec.ts | 49 +- src/shared/lib/PdbUtils.ts | 144 +- src/shared/lib/PromisePlus.ts | 34 +- src/shared/lib/QuerySession.ts | 95 +- src/shared/lib/SampleGeneCache.ts | 27 +- src/shared/lib/Serializer.tsx | 9 +- src/shared/lib/SortUtils.spec.ts | 55 +- src/shared/lib/SortUtils.ts | 13 +- src/shared/lib/SpecUtils.ts | 12 +- src/shared/lib/StoreUtils.spec.ts | 535 +- src/shared/lib/StoreUtils.ts | 1250 ++-- src/shared/lib/TimeUtils.ts | 12 +- src/shared/lib/TypeScriptUtils.ts | 2 +- src/shared/lib/URLWrapper.spec.ts | 596 +- src/shared/lib/URLWrapper.ts | 153 +- src/shared/lib/UuidUtils.spec.ts | 73 +- src/shared/lib/UuidUtils.ts | 52 +- src/shared/lib/VictoryChartUtils.spec.ts | 6 +- src/shared/lib/VictoryChartUtils.ts | 17 +- src/shared/lib/accumulatingDebounce.spec.ts | 235 +- src/shared/lib/accumulatingDebounce.ts | 60 +- src/shared/lib/ajaxQuiet.js | 14 +- src/shared/lib/alterationCountHelpers.spec.ts | 831 +-- src/shared/lib/alterationCountHelpers.ts | 366 +- src/shared/lib/boxPlotUtils.spec.ts | 170 +- src/shared/lib/boxPlotUtils.ts | 130 +- .../BenjaminiHochbergFDRCalculator.spec.ts | 82 +- .../BenjaminiHochbergFDRCalculator.ts | 27 +- src/shared/lib/chunkMapReduce.ts | 10 +- src/shared/lib/cloneJSXWithoutKeyAndRef.tsx | 16 +- .../ComplexKeyCounter.spec.ts | 81 +- .../ComplexKeyCounter.ts | 10 +- .../ComplexKeyGroupsMap.spec.ts | 60 +- .../ComplexKeyGroupsMap.ts | 12 +- .../ComplexKeyMap.spec.ts | 256 +- .../complexKeyDataStructures/ComplexKeyMap.ts | 48 +- .../ComplexKeySet.spec.ts | 158 +- .../complexKeyDataStructures/ComplexKeySet.ts | 21 +- src/shared/lib/consoleLog.ts | 12 +- src/shared/lib/createQueryStore.ts | 42 +- src/shared/lib/customTabs.ts | 45 +- src/shared/lib/errorFormatter.spec.ts | 105 +- src/shared/lib/errorFormatter.ts | 50 +- .../lib/exposeComponentRenderer.spec.tsx | 28 +- src/shared/lib/exposeComponentRenderer.ts | 27 +- src/shared/lib/formSubmit.ts | 16 +- src/shared/lib/getDefaultMolecularProfiles.ts | 90 +- src/shared/lib/getMobxPromiseGroupStatus.ts | 19 +- src/shared/lib/getOverlappingStudies.spec.ts | 75 +- src/shared/lib/getOverlappingStudies.ts | 41 +- src/shared/lib/handleLongUrls.ts | 31 +- src/shared/lib/hashString.ts | 6 +- src/shared/lib/ifNotDefined.ts | 4 +- .../lib/invertIncreasingFunction.spec.ts | 51 +- src/shared/lib/invertIncreasingFunction.ts | 24 +- src/shared/lib/isSampleProfiled.spec.ts | 295 +- src/shared/lib/isSampleProfiled.ts | 59 +- src/shared/lib/onMobxPromise.spec.ts | 164 +- src/shared/lib/onMobxPromise.ts | 28 +- src/shared/lib/onNextRenderFrame.ts | 6 +- src/shared/lib/openSocialAuthWindow.ts | 37 +- src/shared/lib/oql/AccessorsForOqlFilter.ts | 221 +- src/shared/lib/oql/annotateAlterationTypes.ts | 38 +- src/shared/lib/oql/oql-parser.d.ts | 155 +- src/shared/lib/oql/oql-parser.js | 5042 +++++++++-------- src/shared/lib/oql/oql-parser.spec.ts | 1263 ++++- src/shared/lib/oql/oqlfilter.d.ts | 72 +- src/shared/lib/oql/oqlfilter.js | 480 +- src/shared/lib/oql/oqlfilter.spec.ts | 533 +- src/shared/lib/reactionWithPrev.spec.ts | 45 +- src/shared/lib/reactionWithPrev.ts | 20 +- src/shared/lib/redirectHelpers.spec.ts | 44 +- src/shared/lib/redirectHelpers.ts | 106 +- src/shared/lib/seekUrlHash.ts | 10 +- src/shared/lib/setWindowVariable.ts | 2 +- src/shared/lib/sortedFindWith.spec.ts | 203 +- src/shared/lib/sortedFindWith.ts | 10 +- src/shared/lib/textQueryUtils.ts | 288 +- src/shared/lib/tracking.ts | 191 +- src/shared/lib/validateParameters.spec.ts | 41 +- src/shared/lib/validateParameters.ts | 36 +- src/shared/lib/writeTest.ts | 62 +- src/shared/model/AlterationEnrichmentRow.ts | 8 +- src/shared/model/BookmarkLinks.ts | 6 +- src/shared/model/CancerHotspots.ts | 4 +- src/shared/model/Civic.ts | 24 +- src/shared/model/ClinicalInformation.ts | 14 +- src/shared/model/Cosmic.ts | 4 +- src/shared/model/ExpressionEnrichmentRow.ts | 6 +- src/shared/model/Gistic.ts | 6 +- src/shared/model/ITabConfiguration.ts | 28 +- src/shared/model/ITooltipModel.ts | 8 +- src/shared/model/MatchMiner.ts | 16 +- src/shared/model/MutSig.ts | 2 +- src/shared/model/MutationalSignature.ts | 8 +- src/shared/model/MutualExclusivity.ts | 4 +- src/shared/model/MyCancerGenome.ts | 2 +- src/shared/model/OncoKB.ts | 14 +- src/shared/model/PatientSurvival.ts | 2 +- src/shared/model/Pdb.ts | 14 +- src/shared/model/PubMedRecord.ts | 93 +- src/shared/model/VirtualStudy.ts | 10 +- src/shared/polyfill/canvasToBlob.js | 16 +- src/shared/theme/cBioPoralTheme.ts | 381 +- src/test/CivicMockUtils.ts | 283 +- src/test/MutationMockUtils.ts | 71 +- src/test/PdbMockUtils.ts | 40 +- src/test/fetchMockData.js | 66 +- src/testWriter.js | 105 +- 866 files changed, 120136 insertions(+), 69112 deletions(-) diff --git a/src/AppStore.ts b/src/AppStore.ts index 8ff39c9a1b6..575d1a09dd6 100644 --- a/src/AppStore.ts +++ b/src/AppStore.ts @@ -1,30 +1,31 @@ -import {action, computed, observable} from "mobx"; -import {addServiceErrorHandler, getBrowserWindow, remoteData} from "cbioportal-frontend-commons"; -import {initializeAPIClients} from "./config/config"; +import { action, computed, observable } from 'mobx'; +import { + addServiceErrorHandler, + getBrowserWindow, + remoteData, +} from 'cbioportal-frontend-commons'; +import { initializeAPIClients } from './config/config'; import * as _ from 'lodash'; -import internalClient from "shared/api/cbioportalInternalClientInstance"; -import {sendSentryMessage} from "./shared/lib/tracking"; +import internalClient from 'shared/api/cbioportalInternalClientInstance'; +import { sendSentryMessage } from './shared/lib/tracking'; export type SiteError = { - errorObj:any; - dismissed:boolean; - title?:string; + errorObj: any; + dismissed: boolean; + title?: string; }; export class AppStore { - - constructor(){ - + constructor() { getBrowserWindow().me = this; addServiceErrorHandler((error: any) => { - try{ - sendSentryMessage("ERRORHANDLER:" + error); - } catch (ex) {}; - - if (error.status && /400|500/.test(error.status)) { + try { + sendSentryMessage('ERRORHANDLER:' + error); + } catch (ex) {} - sendSentryMessage("ERROR DIALOG SHOWN:" + error); - this.siteErrors.push({errorObj: error, dismissed:false}); + if (error.status && /400|500/.test(error.status)) { + sendSentryMessage('ERROR DIALOG SHOWN:' + error); + this.siteErrors.push({ errorObj: error, dismissed: false }); } }); } @@ -33,35 +34,35 @@ export class AppStore { @observable siteErrors: SiteError[] = []; - @observable userName:string | undefined; + @observable userName: string | undefined; - @observable authMethod:string | undefined; + @observable authMethod: string | undefined; - @computed get isLoggedIn(){ - return _.isString(this.userName) && this.userName !== "anonymousUser"; + @computed get isLoggedIn() { + return _.isString(this.userName) && this.userName !== 'anonymousUser'; } - @computed get logoutUrl(){ - if (this.authMethod === "saml") { - return "saml/logout"; + @computed get logoutUrl() { + if (this.authMethod === 'saml') { + return 'saml/logout'; } else { - return "j_spring_security_logout"; + return 'j_spring_security_logout'; } } - @computed get undismissedSiteErrors(){ - return _.filter(this.siteErrors.slice(), (err)=>!err.dismissed); + @computed get undismissedSiteErrors() { + return _.filter(this.siteErrors.slice(), err => !err.dismissed); } - @computed get isErrorCondition(){ + @computed get isErrorCondition() { return this.undismissedSiteErrors.length > 0; } @action - public dismissErrors(){ - this.siteErrors = this.siteErrors.map((err)=>{ - err.dismissed = true; - return err; + public dismissErrors() { + this.siteErrors = this.siteErrors.map(err => { + err.dismissed = true; + return err; }); } @@ -75,14 +76,21 @@ export class AppStore { } readonly portalVersion = remoteData({ - invoke:async()=>{ - const portalVersionResult = await internalClient.getInfoUsingGET({}); + invoke: async () => { + const portalVersionResult = await internalClient.getInfoUsingGET( + {} + ); if (portalVersionResult && portalVersionResult.portalVersion) { let version = undefined; // try getting version from branch name assume like release-x.y.z - if (portalVersionResult.gitBranch && portalVersionResult.gitBranch.startsWith("release-")) { - let branchVersion = portalVersionResult.gitBranch.split('-')[1]; + if ( + portalVersionResult.gitBranch && + portalVersionResult.gitBranch.startsWith('release-') + ) { + let branchVersion = portalVersionResult.gitBranch.split( + '-' + )[1]; if (branchVersion.split('.').length == 3) { version = branchVersion; } @@ -95,12 +103,12 @@ export class AppStore { } // add v prefix if missing - if (version !== undefined && !version.startsWith("v")) { + if (version !== undefined && !version.startsWith('v')) { version = `v${version}`; } return Promise.resolve(version); } return undefined; - } + }, }); } diff --git a/src/appBootstrapper.jsx b/src/appBootstrapper.jsx index 8243a8ed4ad..56108ee37ce 100755 --- a/src/appBootstrapper.jsx +++ b/src/appBootstrapper.jsx @@ -2,8 +2,8 @@ import React from 'react'; import ReactDOM from 'react-dom'; import { Provider } from 'mobx-react'; import { Router, useRouterHistory } from 'react-router'; -import { createHistory } from 'history' -import { syncHistoryWithStore } from 'mobx-react-router'; +import { createHistory } from 'history'; +import { syncHistoryWithStore } from 'mobx-react-router'; import ExtendedRoutingStore from './shared/lib/ExtendedRouterStore'; import { fetchServerConfig, @@ -11,7 +11,7 @@ import { initializeAppStore, initializeConfiguration, setConfigDefaults, - setServerConfig + setServerConfig, } from './config/config'; import './shared/lib/ajaxQuiet'; @@ -20,15 +20,15 @@ import * as _ from 'lodash'; import $ from 'jquery'; import * as superagent from 'superagent'; import { getHost, buildCBioPortalPageUrl } from './shared/api/urls'; -import AppConfig from "appConfig"; +import AppConfig from 'appConfig'; import browser from 'bowser'; import { setNetworkListener } from './shared/lib/ajaxQuiet'; -import { initializeTracking } from "shared/lib/tracking"; +import { initializeTracking } from 'shared/lib/tracking'; import superagentCache from 'superagent-cache'; -import {getBrowserWindow} from "cbioportal-frontend-commons"; -import {AppStore} from "./AppStore"; -import {handleLongUrls} from "shared/lib/handleLongUrls"; -import "shared/polyfill/canvasToBlob"; +import { getBrowserWindow } from 'cbioportal-frontend-commons'; +import { AppStore } from './AppStore'; +import { handleLongUrls } from 'shared/lib/handleLongUrls'; +import 'shared/polyfill/canvasToBlob'; import mobx from 'mobx'; superagentCache(superagent); @@ -37,39 +37,35 @@ superagentCache(superagent); // it fixes the hash portion of url when cohort patient list is too long handleLongUrls(); - // YOU MUST RUN THESE initialize and then set the public path after initializeConfiguration(); // THIS TELLS WEBPACK BUNDLE LOADER WHERE TO LOAD SPLIT BUNDLES __webpack_public_path__ = AppConfig.frontendUrl; -if (!window.hasOwnProperty("$")) { +if (!window.hasOwnProperty('$')) { window.$ = $; } - - -if (!window.hasOwnProperty("jQuery")) { +if (!window.hasOwnProperty('jQuery')) { window.jQuery = $; } -if (!window.hasOwnProperty("mobx")) { +if (!window.hasOwnProperty('mobx')) { window.mobx = mobx; } // write browser name, version to brody tag if (browser) { - $(document).ready(()=>{ - $("body").addClass(browser.name); + $(document).ready(() => { + $('body').addClass(browser.name); }); } // e2e test specific stuff if (getBrowserWindow().navigator.webdriver) { - - $(document).ready(()=>{ - $("body").addClass("e2etest"); + $(document).ready(() => { + $('body').addClass('e2etest'); window.e2etest = true; }); @@ -82,9 +78,9 @@ window.FRONTEND_COMMIT = COMMIT; // this is special function allowing MSKCC CIS to hide login UI in // portal header -window.postLoadForMskCIS = function(){ +window.postLoadForMskCIS = function() { AppConfig.hide_login = true; -} +}; // make sure lodash doesn't overwrite (or set) global underscore _.noConflict(); @@ -92,7 +88,7 @@ _.noConflict(); const routingStore = new ExtendedRoutingStore(); const history = useRouterHistory(createHistory)({ - basename: AppConfig.basePath || "" + basename: AppConfig.basePath || '', }); const syncedHistory = syncHistoryWithStore(history, routingStore); @@ -100,7 +96,7 @@ const syncedHistory = syncHistoryWithStore(history, routingStore); const stores = { // Key can be whatever you want routing: routingStore, - appStore:new AppStore() + appStore: new AppStore(), }; window.globalStores = stores; @@ -109,21 +105,25 @@ const end = superagent.Request.prototype.end; let redirecting = false; -superagent.Request.prototype.end = function (callback) { +superagent.Request.prototype.end = function(callback) { return end.call(this, (error, response) => { - if (redirecting) { return; } if (response && response.statusCode === 401) { - var storageKey = `redirect${Math.floor(Math.random() * 1000000000000)}` + var storageKey = `redirect${Math.floor( + Math.random() * 1000000000000 + )}`; localStorage.setItem(storageKey, window.location.href); // build URL with a reference to storage key so that /restore route can restore it after login const loginUrl = buildCBioPortalPageUrl({ query: { - "spring-security-redirect":buildCBioPortalPageUrl({ pathname:"restore", query: { key: storageKey} }) - } + 'spring-security-redirect': buildCBioPortalPageUrl({ + pathname: 'restore', + query: { key: storageKey }, + }), + }, }); redirecting = true; @@ -136,22 +136,17 @@ superagent.Request.prototype.end = function (callback) { window.routingStore = routingStore; - let render = () => { - if (!getBrowserWindow().navigator.webdriver) initializeTracking(); - const rootNode = document.getElementById("reactRoot"); + const rootNode = document.getElementById('reactRoot'); ReactDOM.render( - - - - , rootNode); - - + + , + rootNode + ); }; if (__DEBUG__ && module.hot) { @@ -162,15 +157,14 @@ if (__DEBUG__ && module.hot) { } $(document).ready(async () => { - // we show blank page if the window.name is "blank" - if (window.name === "blank") { + if (window.name === 'blank') { return; } // we use rawServerConfig (written by JSP) if it is present // or fetch from config service if not // need to use jsonp, so use jquery - let config = window.rawServerConfig || await fetchServerConfig(); + let config = window.rawServerConfig || (await fetchServerConfig()); setServerConfig(config); @@ -178,7 +172,7 @@ $(document).ready(async () => { initializeAPIClients(); - initializeAppStore(stores.appStore,config); + initializeAppStore(stores.appStore, config); render(); diff --git a/src/appShell/App/Container.tsx b/src/appShell/App/Container.tsx index efa62a753af..a6d0f3fb10f 100644 --- a/src/appShell/App/Container.tsx +++ b/src/appShell/App/Container.tsx @@ -2,19 +2,23 @@ import * as _ from 'lodash'; import * as React from 'react'; import '../../globalStyles/prefixed-global.scss'; -import PortalHeader from "./PortalHeader"; -import {getBrowserWindow, isWebdriver} from "cbioportal-frontend-commons"; -import {observer} from "mobx-react"; +import PortalHeader from './PortalHeader'; +import { getBrowserWindow, isWebdriver } from 'cbioportal-frontend-commons'; +import { observer } from 'mobx-react'; -import LoadingIndicator from "../../shared/components/loadingIndicator/LoadingIndicator"; -import AppConfig from "appConfig"; -import Helmet from "react-helmet"; -import {computed} from "mobx"; +import LoadingIndicator from '../../shared/components/loadingIndicator/LoadingIndicator'; +import AppConfig from 'appConfig'; +import Helmet from 'react-helmet'; +import { computed } from 'mobx'; import { If, Else, Then } from 'react-if'; -import UserMessager from "shared/components/userMessager/UserMessage"; -import {formatErrorLog, formatErrorTitle, formatErrorMessages} from "shared/lib/errorFormatter"; -import {buildCBioPortalPageUrl} from "shared/api/urls"; -import ErrorScreen from "shared/components/errorScreen/ErrorScreen"; +import UserMessager from 'shared/components/userMessager/UserMessage'; +import { + formatErrorLog, + formatErrorTitle, + formatErrorMessages, +} from 'shared/lib/errorFormatter'; +import { buildCBioPortalPageUrl } from 'shared/api/urls'; +import ErrorScreen from 'shared/components/errorScreen/ErrorScreen'; import { ServerConfigHelpers } from 'config/config'; interface IContainerProps { @@ -24,20 +28,20 @@ interface IContainerProps { @observer export default class Container extends React.Component { - - private get routingStore(){ + private get routingStore() { return getBrowserWindow().routingStore; } - private get appStore(){ + private get appStore() { return getBrowserWindow().globalStores.appStore; } renderChildren() { - const childProps = {...this.props}; - const {children} = this.props; - return React.Children.map(children, - c => React.cloneElement(c as React.ReactElement, childProps)); + const childProps = { ...this.props }; + const { children } = this.props; + return React.Children.map(children, c => + React.cloneElement(c as React.ReactElement, childProps) + ); } render() { @@ -45,12 +49,20 @@ export default class Container extends React.Component { return (
As of version 3.0.0, all cBioPortal installations require a session service. Please review these instructions for how to do so. https://docs.cbioportal.org/2.1.2-deploy-without-docker/deploying#run-cbioportal-session-service -

} + title={'No session service configured'} + body={ +

+ As of version 3.0.0, all cBioPortal + installations require a session service. Please + review these instructions for how to do so.{' '} + + https://docs.cbioportal.org/2.1.2-deploy-without-docker/deploying#run-cbioportal-session-service + +

+ } />
- ) + ); } return ( @@ -58,23 +70,39 @@ export default class Container extends React.Component { {AppConfig.serverConfig.skin_title} - +
- +
Return to homepage} - errorLog={formatErrorLog(this.appStore.undismissedSiteErrors)} - errorMessages={formatErrorMessages(this.appStore.undismissedSiteErrors)} + title={ + formatErrorTitle( + this.appStore.undismissedSiteErrors + ) || + 'Oops. There was an error retrieving data.' + } + body={ + + Return to homepage + + } + errorLog={formatErrorLog( + this.appStore.undismissedSiteErrors + )} + errorMessages={formatErrorMessages( + this.appStore.undismissedSiteErrors + )} />
@@ -88,5 +116,3 @@ export default class Container extends React.Component { ); } } - - diff --git a/src/appShell/App/PortalFooter.tsx b/src/appShell/App/PortalFooter.tsx index 6dcd7dfc652..831a78b08bd 100644 --- a/src/appShell/App/PortalFooter.tsx +++ b/src/appShell/App/PortalFooter.tsx @@ -1,105 +1,233 @@ import * as React from 'react'; -import AppConfig from "appConfig"; +import AppConfig from 'appConfig'; import { If } from 'react-if'; // tslint:disable-next-line:no-import-side-effect import './footer.scss'; import _ from 'lodash'; import { Link } from 'react-router'; -import {AppStore} from "../../AppStore"; -import {observer} from "mobx-react"; - -@observer export default class PortalFooter extends React.Component<{appStore:AppStore}, {}> { +import { AppStore } from '../../AppStore'; +import { observer } from 'mobx-react'; +@observer +export default class PortalFooter extends React.Component< + { appStore: AppStore }, + {} +> { render() { - var version; - if (this.props.appStore.portalVersion.isComplete && !this.props.appStore.portalVersion.isError && this.props.appStore.portalVersion.result){ - version = this.props.appStore.portalVersion.result; - } - else{ - version = "--" - } - if (AppConfig.serverConfig.skin_footer && !_.isEmpty(AppConfig.serverConfig.skin_footer)) { - return ( - - ); - } else { - return ( -