@jbrowse/core 4.3.0 → 5.0.0-beta.10
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +1994 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +14 -3
- package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +36 -23
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +10 -7
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +124 -21
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.d.ts +2 -8
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js +4 -4
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts +1 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js +2 -5
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.d.ts +1 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js +4 -4
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.d.ts +12 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +19 -5
- package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +18 -23
- package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.d.ts +1 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +19 -40
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +9 -6
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +33 -30
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.d.ts +11 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.js +11 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.d.ts +8 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.js +24 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +19 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.d.ts +4 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.js +17 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +5 -3
- package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +8 -6
- package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
- package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
- package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +7 -2
- package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +15 -20
- package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.d.ts +16 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.js +50 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +0 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +9 -10
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +35 -24
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +3 -3
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +20 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +62 -63
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +69 -59
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
- package/esm/BaseFeatureWidget/configSchema.d.ts +1 -1
- package/esm/BaseFeatureWidget/configSchema.js +1 -1
- package/esm/BaseFeatureWidget/formatDetails.d.ts +22 -0
- package/esm/BaseFeatureWidget/formatDetails.js +82 -0
- package/esm/BaseFeatureWidget/index.d.ts +4 -1
- package/esm/BaseFeatureWidget/index.js +2 -2
- package/esm/BaseFeatureWidget/stateModelFactory.d.ts +102 -71
- package/esm/BaseFeatureWidget/stateModelFactory.js +162 -63
- package/esm/BaseFeatureWidget/types.d.ts +15 -8
- package/esm/BaseFeatureWidget/util.d.ts +2 -37
- package/esm/BaseFeatureWidget/util.js +4 -85
- package/esm/CorePlugin.js +12 -7
- package/esm/PhasedScheduler.d.ts +4 -2
- package/esm/PhasedScheduler.js +18 -2
- package/esm/Plugin.d.ts +6 -1
- package/esm/Plugin.js +7 -0
- package/esm/PluginLoader.d.ts +55 -44
- package/esm/PluginLoader.js +290 -90
- package/esm/PluginManager.d.ts +476 -57
- package/esm/PluginManager.js +480 -91
- package/esm/ReExports/MuiDataGridReExports.d.ts +3 -2
- package/esm/ReExports/MuiDataGridReExports.js +58 -130
- package/esm/ReExports/MuiReExports.d.ts +3 -134
- package/esm/ReExports/MuiReExports.js +43 -16
- package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
- package/esm/ReExports/MuiStylesReExports.js +55 -0
- package/esm/ReExports/coreModules.generated.d.ts +2 -0
- package/esm/ReExports/coreModules.generated.js +528 -0
- package/esm/ReExports/coreWorkerModules.generated.d.ts +2 -0
- package/esm/ReExports/coreWorkerModules.generated.js +488 -0
- package/esm/ReExports/frameworkModules.d.ts +2 -0
- package/esm/ReExports/frameworkModules.js +68 -0
- package/esm/ReExports/frameworkShared.d.ts +12 -0
- package/esm/ReExports/frameworkShared.js +16 -0
- package/esm/ReExports/frameworkWorkerModules.generated.d.ts +2 -0
- package/esm/ReExports/frameworkWorkerModules.generated.js +130 -0
- package/esm/ReExports/lazify.d.ts +2 -2
- package/esm/ReExports/lazify.js +16 -3
- package/esm/ReExports/list.js +433 -160
- package/esm/ReExports/modules.d.ts +1 -1
- package/esm/ReExports/modules.js +10 -146
- package/esm/ReExports/muiComponentNames.d.ts +18 -0
- package/esm/ReExports/muiComponentNames.js +130 -0
- package/esm/ReExports/registry.d.ts +3 -0
- package/esm/ReExports/registry.js +46 -0
- package/esm/ReExports/uiStub.d.ts +3 -0
- package/esm/ReExports/uiStub.js +33 -0
- package/esm/ReExports/workerModules.d.ts +2 -0
- package/esm/ReExports/workerModules.js +11 -0
- package/esm/TextSearch/BaseResults.d.ts +20 -21
- package/esm/TextSearch/BaseResults.js +8 -33
- package/esm/TextSearch/TextSearchManager.d.ts +30 -36
- package/esm/TextSearch/TextSearchManager.js +138 -44
- package/esm/TextSearch/places.d.ts +12 -0
- package/esm/TextSearch/places.js +94 -0
- package/esm/assemblyManager/assembly.d.ts +310 -35
- package/esm/assemblyManager/assembly.js +554 -263
- package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
- package/esm/assemblyManager/assemblyAdapters.js +24 -0
- package/esm/assemblyManager/assemblyConfigSchema.d.ts +135 -19
- package/esm/assemblyManager/assemblyConfigSchema.js +205 -23
- package/esm/assemblyManager/assemblyManager.d.ts +586 -323
- package/esm/assemblyManager/assemblyManager.js +352 -51
- package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +39 -0
- package/esm/assemblyManager/expandAssemblyConfigShorthand.js +114 -0
- package/esm/assemblyManager/geneticCodes.d.ts +21 -0
- package/esm/assemblyManager/geneticCodes.js +44 -0
- package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +19 -0
- package/esm/assemblyManager/getSequenceAdapterConfig.js +22 -0
- package/esm/assemblyManager/index.d.ts +1 -1
- package/esm/assemblyManager/index.js +2 -2
- package/esm/assemblyManager/indexAssemblyNames.d.ts +9 -0
- package/esm/assemblyManager/indexAssemblyNames.js +22 -0
- package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
- package/esm/assemblyManager/loadRefNameMap.js +75 -0
- package/esm/assemblyManager/refNameColors.d.ts +1 -0
- package/esm/assemblyManager/refNameColors.js +32 -0
- package/esm/assemblyManager/refNameMapKey.d.ts +7 -0
- package/esm/assemblyManager/refNameMapKey.js +12 -0
- package/esm/assemblyManager/refNameMaps.d.ts +26 -0
- package/esm/assemblyManager/refNameMaps.js +87 -0
- package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
- package/esm/assemblyManager/refNameMismatch.js +66 -0
- package/esm/checkPlugins.d.ts +13 -0
- package/esm/checkPlugins.js +98 -0
- package/esm/configuration/bamIndexFields.d.ts +49 -0
- package/esm/configuration/bamIndexFields.js +41 -0
- package/esm/configuration/configurationSchema.d.ts +194 -29
- package/esm/configuration/configurationSchema.js +439 -145
- package/esm/configuration/configurationSchemaUnion.d.ts +39 -0
- package/esm/configuration/configurationSchemaUnion.js +56 -0
- package/esm/configuration/configurationSlot.d.ts +373 -30
- package/esm/configuration/configurationSlot.js +231 -224
- package/esm/configuration/fillLocations.d.ts +14 -0
- package/esm/configuration/fillLocations.js +14 -0
- package/esm/configuration/formatAboutConfigSchema.d.ts +41 -0
- package/esm/configuration/formatAboutConfigSchema.js +58 -0
- package/esm/configuration/formatDetailsConfigSchema.d.ts +54 -0
- package/esm/configuration/formatDetailsConfigSchema.js +87 -0
- package/esm/configuration/fullConfSnapshot.d.ts +13 -0
- package/esm/configuration/fullConfSnapshot.js +44 -0
- package/esm/configuration/getConf.d.ts +92 -0
- package/esm/configuration/getConf.js +141 -0
- package/esm/configuration/index.d.ts +32 -3
- package/esm/configuration/index.js +27 -2
- package/esm/configuration/indexType.d.ts +26 -0
- package/esm/configuration/indexType.js +38 -0
- package/esm/configuration/mergeFormatCallbacks.d.ts +14 -0
- package/esm/configuration/mergeFormatCallbacks.js +27 -0
- package/esm/configuration/readConfObject.d.ts +34 -0
- package/esm/configuration/readConfObject.js +118 -0
- package/esm/configuration/requirements.d.ts +37 -0
- package/esm/configuration/requirements.js +88 -0
- package/esm/configuration/schemaRegistry.d.ts +52 -0
- package/esm/configuration/schemaRegistry.js +48 -0
- package/esm/configuration/schemaTypes.d.ts +39 -0
- package/esm/configuration/schemaTypes.js +105 -0
- package/esm/configuration/slotFacade.d.ts +65 -0
- package/esm/configuration/slotFacade.js +110 -0
- package/esm/configuration/slotValueUtils.d.ts +17 -0
- package/esm/configuration/slotValueUtils.js +25 -0
- package/esm/configuration/snapshotPreprocess.d.ts +43 -0
- package/esm/configuration/snapshotPreprocess.js +161 -0
- package/esm/configuration/tabixIndexFields.d.ts +70 -0
- package/esm/configuration/tabixIndexFields.js +62 -0
- package/esm/configuration/tabixShorthand.d.ts +51 -0
- package/esm/configuration/tabixShorthand.js +72 -0
- package/esm/configuration/types.d.ts +315 -13
- package/esm/configuration/uriShorthand.d.ts +9 -0
- package/esm/configuration/uriShorthand.js +16 -0
- package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +19 -11
- package/esm/data_adapters/BaseAdapter/BaseAdapter.js +19 -18
- package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +158 -7
- package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +164 -29
- package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
- package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
- package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
- package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
- package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
- package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
- package/esm/data_adapters/BaseAdapter/featureDensity.d.ts +40 -0
- package/esm/data_adapters/BaseAdapter/featureDensity.js +31 -0
- package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
- package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
- package/esm/data_adapters/BaseAdapter/index.d.ts +28 -6
- package/esm/data_adapters/BaseAdapter/index.js +6 -5
- package/esm/data_adapters/BaseAdapter/rowSources.d.ts +37 -0
- package/esm/data_adapters/BaseAdapter/rowSources.js +7 -0
- package/esm/data_adapters/BaseAdapter/stats.d.ts +37 -5
- package/esm/data_adapters/BaseAdapter/stats.js +89 -24
- package/esm/data_adapters/BaseAdapter/types.d.ts +11 -13
- package/esm/data_adapters/BaseAdapter/types.js +1 -0
- package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
- package/esm/data_adapters/BaseAdapter/util.js +14 -3
- package/esm/data_adapters/BaseAdapter/zoomRange.d.ts +10 -0
- package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
- package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +5 -5
- package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +34 -6
- package/esm/data_adapters/CytobandAdapter/configSchema.js +47 -17
- package/esm/data_adapters/CytobandAdapter/index.js +3 -3
- package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
- package/esm/data_adapters/adapterSessionRefcount.js +96 -0
- package/esm/data_adapters/dataAdapterCache.d.ts +53 -2
- package/esm/data_adapters/dataAdapterCache.js +99 -25
- package/esm/data_adapters/getFeatureAdapter.d.ts +24 -0
- package/esm/data_adapters/getFeatureAdapter.js +27 -0
- package/esm/data_adapters/getSequenceSubAdapter.d.ts +19 -0
- package/esm/data_adapters/getSequenceSubAdapter.js +42 -0
- package/esm/pluggableElementTypes/AdapterType.d.ts +57 -7
- package/esm/pluggableElementTypes/AdapterType.js +44 -5
- package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
- package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
- package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
- package/esm/pluggableElementTypes/ConnectionType.js +1 -1
- package/esm/pluggableElementTypes/DisplayType.d.ts +54 -14
- package/esm/pluggableElementTypes/DisplayType.js +30 -7
- package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
- package/esm/pluggableElementTypes/LazyStateModelElement.d.ts +32 -0
- package/esm/pluggableElementTypes/LazyStateModelElement.js +77 -0
- package/esm/pluggableElementTypes/PluggableElementBase.d.ts +11 -0
- package/esm/pluggableElementTypes/PluggableElementBase.js +11 -0
- package/esm/pluggableElementTypes/RpcMethodType.d.ts +142 -12
- package/esm/pluggableElementTypes/RpcMethodType.js +279 -98
- package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +18 -9
- package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
- package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
- package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
- package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
- package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
- package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +7 -7
- package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
- package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
- package/esm/pluggableElementTypes/TrackType.js +1 -1
- package/esm/pluggableElementTypes/ViewType.d.ts +22 -5
- package/esm/pluggableElementTypes/ViewType.js +40 -5
- package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
- package/esm/pluggableElementTypes/WidgetType.js +1 -1
- package/esm/pluggableElementTypes/addMenuItems.d.ts +88 -0
- package/esm/pluggableElementTypes/addMenuItems.js +82 -0
- package/esm/pluggableElementTypes/extendElementType.d.ts +29 -0
- package/esm/pluggableElementTypes/extendElementType.js +72 -0
- package/esm/pluggableElementTypes/index.d.ts +8 -7
- package/esm/pluggableElementTypes/index.js +24 -14
- package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +80 -15
- package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
- package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +643 -84
- package/esm/pluggableElementTypes/models/BaseDisplayModel.js +230 -60
- package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +246 -37
- package/esm/pluggableElementTypes/models/BaseTrackModel.js +416 -107
- package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +236 -16
- package/esm/pluggableElementTypes/models/BaseViewModel.js +154 -16
- package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +169 -25
- package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
- package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +178 -0
- package/esm/pluggableElementTypes/models/assertDisplayContract.js +239 -0
- package/esm/pluggableElementTypes/models/baseConnectionConfig.d.ts +26 -8
- package/esm/pluggableElementTypes/models/baseConnectionConfig.js +18 -2
- package/esm/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +31 -17
- package/esm/pluggableElementTypes/models/baseInternetAccountConfig.js +23 -2
- package/esm/pluggableElementTypes/models/baseTrackConfig.d.ts +142 -65
- package/esm/pluggableElementTypes/models/baseTrackConfig.js +215 -90
- package/esm/pluggableElementTypes/models/components/SaveTrackData.d.ts +3 -8
- package/esm/pluggableElementTypes/models/components/SaveTrackData.js +111 -139
- package/esm/pluggableElementTypes/models/components/fetchTrackData.d.ts +54 -0
- package/esm/pluggableElementTypes/models/components/fetchTrackData.js +83 -0
- package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.d.ts +50 -0
- package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.js +147 -0
- package/esm/pluggableElementTypes/models/index.d.ts +5 -3
- package/esm/pluggableElementTypes/models/index.js +9 -8
- package/esm/pluggableElementTypes/models/migrateTrackConfig.d.ts +48 -0
- package/esm/pluggableElementTypes/models/migrateTrackConfig.js +114 -0
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.js +75 -7
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.d.ts +10 -3
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +272 -100
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.d.ts +6 -1
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.js +70 -74
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- package/esm/util/useFetchPlugins.d.ts +16 -0
- package/esm/util/useFetchPlugins.js +18 -0
- package/esm/util/useMeasure.d.ts +11 -1
- package/esm/util/useMeasure.js +20 -6
- package/esm/util/usePanZoom.d.ts +75 -0
- package/esm/util/usePanZoom.js +175 -0
- package/esm/util/usePanelVirtualScroll.d.ts +9 -0
- package/esm/util/usePanelVirtualScroll.js +15 -0
- package/esm/util/usePointerDrag.d.ts +37 -0
- package/esm/util/usePointerDrag.js +61 -0
- package/esm/util/useRafCommit.d.ts +4 -0
- package/esm/util/useRafCommit.js +50 -0
- package/esm/util/useResizeDrag.d.ts +91 -0
- package/esm/util/useResizeDrag.js +105 -0
- package/esm/util/useRowVirtualScroll.d.ts +9 -0
- package/esm/util/useRowVirtualScroll.js +22 -0
- package/esm/util/useVirtualScrollWheel.d.ts +23 -0
- package/esm/util/useVirtualScrollWheel.js +74 -0
- package/esm/util/viewHighlights.d.ts +3 -0
- package/esm/util/viewHighlights.js +5 -0
- package/esm/util/viewStatus.d.ts +90 -0
- package/esm/util/viewStatus.js +54 -0
- package/esm/util/virtualRange.d.ts +36 -0
- package/esm/util/virtualRange.js +26 -0
- package/esm/util/webStorage.d.ts +26 -0
- package/esm/util/webStorage.js +92 -0
- package/esm/util/wheelZoom.d.ts +65 -0
- package/esm/util/wheelZoom.js +297 -0
- package/esm/util/whenViewSettled.d.ts +74 -0
- package/esm/util/whenViewSettled.js +77 -0
- package/esm/util/withFeatureDetails.d.ts +34 -0
- package/esm/util/withFeatureDetails.js +59 -0
- package/esm/util/withLaunchInput.d.ts +174 -0
- package/esm/util/withLaunchInput.js +274 -0
- package/package.json +290 -820
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +0 -2
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +0 -14
- package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +0 -7
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +0 -80
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.js +0 -583
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +0 -141
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.js +0 -1116
- package/esm/ReExports/BaseFeatureDetails.d.ts +0 -1
- package/esm/ReExports/BaseFeatureDetails.js +0 -9
- package/esm/ReExports/DataGrid.d.ts +0 -1
- package/esm/ReExports/DataGrid.js +0 -1
- package/esm/ReExports/index.d.ts +0 -1
- package/esm/ReExports/index.js +0 -1
- package/esm/configuration/util.d.ts +0 -10
- package/esm/configuration/util.js +0 -123
- package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
- package/esm/data_adapters/util.d.ts +0 -1
- package/esm/data_adapters/util.js +0 -6
- package/esm/pluggableElementTypes/GlyphType.d.ts +0 -43
- package/esm/pluggableElementTypes/GlyphType.js +0 -18
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +0 -5
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +0 -17
- package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +0 -52
- package/esm/pluggableElementTypes/renderers/BoxRendererType.js +0 -78
- package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +0 -4
- package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +0 -4
- package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -58
- package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +0 -77
- package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +0 -31
- package/esm/pluggableElementTypes/renderers/LayoutSession.js +0 -40
- package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
- package/esm/pluggableElementTypes/renderers/RendererType.js +0 -20
- package/esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +0 -58
- package/esm/pluggableElementTypes/renderers/ServerSideRendererType.js +0 -108
- package/esm/pluggableElementTypes/renderers/index.d.ts +0 -6
- package/esm/pluggableElementTypes/renderers/index.js +0 -6
- package/esm/pluggableElementTypes/renderers/util.d.ts +0 -3
- package/esm/pluggableElementTypes/renderers/util.js +0 -14
- package/esm/rpc/baseRpcConfig.d.ts +0 -8
- package/esm/rpc/baseRpcConfig.js +0 -10
- package/esm/rpc/mainThreadRpcConfig.d.ts +0 -8
- package/esm/rpc/mainThreadRpcConfig.js +0 -8
- package/esm/rpc/methods/CoreGetFeatureDensityStats.d.ts +0 -17
- package/esm/rpc/methods/CoreGetFeatureDensityStats.js +0 -25
- package/esm/rpc/methods/CoreGetFeatureDetails.d.ts +0 -11
- package/esm/rpc/methods/CoreGetFeatureDetails.js +0 -24
- package/esm/rpc/methods/CoreGetFileInfo.d.ts +0 -9
- package/esm/rpc/methods/CoreGetFileInfo.js +0 -15
- package/esm/rpc/methods/CoreRender.d.ts +0 -14
- package/esm/rpc/methods/CoreRender.js +0 -40
- package/esm/rpc/methods/CoreSaveFeatureData.d.ts +0 -16
- package/esm/rpc/methods/CoreSaveFeatureData.js +0 -32
- package/esm/rpc/methods/util.d.ts +0 -15
- package/esm/rpc/methods/util.js +0 -7
- package/esm/rpc/webWorkerRpcConfig.d.ts +0 -8
- package/esm/rpc/webWorkerRpcConfig.js +0 -8
- package/esm/ui/MenuButton.d.ts +0 -1
- package/esm/ui/MenuButton.js +0 -1
- package/esm/ui/MenuItems.d.ts +0 -15
- package/esm/ui/MenuItems.js +0 -59
- package/esm/ui/useEvent.d.ts +0 -1
- package/esm/ui/useEvent.js +0 -10
- package/esm/util/blobToDataURL.d.ts +0 -1
- package/esm/util/blobToDataURL.js +0 -14
- package/esm/util/compositeMap.d.ts +0 -11
- package/esm/util/compositeMap.js +0 -59
- package/esm/util/flatqueue/index.d.ts +0 -11
- package/esm/util/flatqueue/index.js +0 -61
- package/esm/util/layouts/BaseLayout.d.ts +0 -30
- package/esm/util/layouts/MultiLayout.d.ts +0 -12
- package/esm/util/layouts/MultiLayout.js +0 -40
- package/esm/util/layouts/PileupLayout.d.ts +0 -41
- package/esm/util/layouts/PileupLayout.js +0 -202
- package/esm/util/layouts/PrecomputedLayout.d.ts +0 -30
- package/esm/util/layouts/PrecomputedLayout.js +0 -71
- package/esm/util/layouts/SceneGraph.d.ts +0 -31
- package/esm/util/layouts/SceneGraph.js +0 -121
- package/esm/util/makeAbortableReaction.d.ts +0 -3
- package/esm/util/makeAbortableReaction.js +0 -47
- package/esm/util/map-obj/index.d.ts +0 -13
- package/esm/util/map-obj/index.js +0 -92
- package/esm/util/nextTick.d.ts +0 -1
- package/esm/util/nextTick.js +0 -3
- package/esm/util/offscreenCanvasGetSerializingSvg.d.ts +0 -5
- package/esm/util/offscreenCanvasGetSerializingSvg.js +0 -9
- package/esm/util/offscreenCanvasUtils.d.ts +0 -12
- package/esm/util/offscreenCanvasUtils.js +0 -19
- package/esm/util/renderToAbstractCanvas.d.ts +0 -17
- package/esm/util/renderToAbstractCanvas.js +0 -53
- package/esm/util/stopToken.d.ts +0 -19
- package/esm/util/stopToken.js +0 -90
- package/esm/util/transferables.d.ts +0 -2
- package/esm/util/transferables.js +0 -35
- package/esm/util/tss-react/mui/index.d.ts +0 -1
- package/esm/util/tss-react/mui/index.js +0 -1
- package/esm/util/tss-react/mui/mui.d.ts +0 -10
- package/esm/util/tss-react/mui/mui.js +0 -5
- package/esm/util/when.d.ts +0 -1
- package/esm/util/when.js +0 -1
- /package/esm/{BaseFeatureWidget/BaseFeatureDetail/types.js → data_adapters/BaseAdapter/CytobandAdapter.js} +0 -0
- /package/esm/data_adapters/BaseAdapter/{BaseOptions.js → zoomRange.js} +0 -0
- /package/esm/{util/layouts/BaseLayout.js → rpc/RpcRegistry.js} +0 -0
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import type { IStateTreeNode } from '@jbrowse/mobx-state-tree';
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/** what a diagnostic calls the view: its snapshot `type`, or the model name */
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export declare function viewLabel(self: IStateTreeNode): string;
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/**
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* What every surface calls this mistake. A session spec launches a view without
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* through its own session rather than through the sink below — one wording, so
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export declare function unknownKeysMessage(label: string, keys: string[]): string;
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/** Why a settings key `applyDisplaySettings` was handed wrote nothing. */
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export type UnappliedReason = 'no-slot' | 'setter-only' | 'display-type';
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export interface UnappliedSetting {
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key: string;
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reason: UnappliedReason;
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}
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/** The action `setter-only` names: `height` -> `setHeight`. */
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export declare function displaySetterName(key: string): string;
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/**
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* What a surface calls a key the display has an action for but no slot. Its own
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export declare function setterOnlyMessage(label: string, keys: string[]): string;
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/**
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* Name the keys a view was handed and could not place, from the partition
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export declare function reportUnknownKeys(self: IStateTreeNode, keys: string[]): void;
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/**
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export declare function reportMalformedRows(self: IStateTreeNode, keys: string[]): void;
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/**
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* What every surface calls v4's nested `init`. v5 takes every setting directly
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* on the view object and unwraps the nesting on the way in, so the settings
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* still arrive — this names the spelling to fix while they do.
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export declare function reportLegacyInit(self: IStateTreeNode): void;
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/** what a diagnostic calls the view: its snapshot `type`, or the model name */
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export function viewLabel(self) {
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return self.type ?? getType(self).name;
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}
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/**
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* What every surface calls this mistake. A session spec launches a view without
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* ever building a snapshot, so it classifies its own keys and reports them
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* through its own session rather than through the sink below — one wording, so
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* a typo reads the same whether it was written in a config or in a URL.
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*/
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export function unknownKeysMessage(label, keys) {
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return `${label} ignored unknown key(s): ${keys.join(', ')}`;
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}
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/** The action `setter-only` names: `height` -> `setHeight`. */
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}
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/**
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* What a surface calls a key the display has an action for but no slot. Its own
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* sentence rather than `unknownKeysMessage`'s: the display does take the
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* setting, just not written this way, and saying "unknown key" over a key whose
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* setter we name in the same breath contradicts itself.
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export function setterOnlyMessage(label, keys) {
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return `${label} did not apply ${keys.join(', ')}: no config slot takes ${keys.length > 1 ? 'them' : 'it'}. Call ${keys.map(displaySetterName).join(', ')} on the display instead.`;
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}
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/**
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* Name the keys a view was handed and could not place, from the partition
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*/
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return;
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}
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const message = unknownKeysMessage(viewLabel(self), keys);
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try {
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getNotificationSink(self).notify(message, 'warning');
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}
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catch {
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}
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}
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/**
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* Name the row lists a view refused whole. `withLaunchInput` splits an authored
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* array into the recipes a launcher resolves and the built snapshots MST
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* restores, per entry — but a row list is indexed against the view's `levels`
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* and per-level tracks, so a list holding both kinds has no correct split and
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* is refused rather than renumbered.
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*/
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export function reportMalformedRows(self, keys) {
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return;
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const message = `${viewLabel(self)} refused ${keys.join(', ')}: the list mixes built view snapshots with recipes to open one, and the rows index against the levels between them. Write all of them one way.`;
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/**
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* What every surface calls v4's nested `init`. v5 takes every setting directly
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* still arrive — this names the spelling to fix while they do.
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export function legacyInitMessage(label) {
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return `${label} nests its settings under "init", which is deprecated: write every setting directly on the view object.`;
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}
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* nothing for a visitor to act on and a warning toast over a working view is
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* noise. `jbrowse validate` is where the author of the config hears about it.
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// Deliberately its own entry rather than a name on the util barrel:
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export declare function useEventCallback<Args extends unknown[], Return>(fn: (...args: Args) => Return): (...args: Args) => Return;
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//
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useLayoutEffect(() => {
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});
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import type { AbstractSessionModel
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export declare function useFeatureSequence({ session,
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assemblyName: string;
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import type { AbstractSessionModel } from './types/index.ts';
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export declare function useFeatureSequence({ session, start, end, refName, upDownBp, forceLoad, assemblyName, }: {
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assemblyName: string | undefined;
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session?: AbstractSessionModel;
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start: number;
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end: number;
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refName: string;
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forceLoad: boolean;
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shouldFetch?: boolean;
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}): {
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sequence: {
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error: string;
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seq?: undefined;
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upstream?: undefined;
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downstream?: undefined;
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error?: undefined;
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error: string;
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loading: boolean;
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error: unknown;
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status: import("./progress.ts").RpcStatus | undefined;
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};
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@@ -1,87 +1,65 @@
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import {
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import {
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import { fetchSeq } from './fetchSeq.js';
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import { createStatusFanOut } from './progress.js';
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import { useFetch } from './useFetch.js';
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4
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const BPLIMIT = 20_000_000;
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export function useFeatureSequence({ session,
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const
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const
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}
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const start = feature.get('start');
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const end = feature.get('end');
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const refName = feature.get('refName');
|
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return {
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export function useFeatureSequence({ session, start, end, refName, upDownBp, forceLoad, assemblyName, }) {
|
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|
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const guard = session && assemblyName ? { session, assemblyName } : null;
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const { data: sequence, error, isLoading: loading, status, } = useFetch(guard
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? [
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guard.assemblyName,
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refName,
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start,
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end,
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refName,
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assemblyName,
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upDownBp,
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forceLoad,
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start,
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end,
|
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49
|
-
refName,
|
|
50
|
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assemblyName,
|
|
51
|
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session: session,
|
|
52
|
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}),
|
|
53
|
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fetchSeq({
|
|
54
|
-
start: Math.max(0, b),
|
|
16
|
+
]
|
|
17
|
+
: null, guard
|
|
18
|
+
? async (_name, _asm, _ref, _start, _end, _upDown, _force, signal, statusCallback) => {
|
|
19
|
+
const { session: s, assemblyName: asmName } = guard;
|
|
20
|
+
if (!forceLoad && end - start > BPLIMIT) {
|
|
21
|
+
return {
|
|
22
|
+
error: `Genomic sequence larger than ${BPLIMIT}bp, use "force load" button to display`,
|
|
23
|
+
};
|
|
24
|
+
}
|
|
25
|
+
// three concurrent reads sharing one status field, so each gets its
|
|
26
|
+
// own slot and they aggregate into one bar
|
|
27
|
+
const slot = createStatusFanOut(statusCallback);
|
|
28
|
+
const [seq, upstream, downstream] = await Promise.all([
|
|
29
|
+
fetchSeq({
|
|
30
|
+
start,
|
|
31
|
+
end,
|
|
32
|
+
refName,
|
|
33
|
+
assemblyName: asmName,
|
|
34
|
+
session: s,
|
|
35
|
+
signal,
|
|
36
|
+
statusCallback: slot(),
|
|
37
|
+
}),
|
|
38
|
+
upDownBp > 0
|
|
39
|
+
? fetchSeq({
|
|
40
|
+
start: Math.max(0, start - upDownBp),
|
|
55
41
|
end: start,
|
|
56
42
|
refName,
|
|
57
|
-
assemblyName,
|
|
58
|
-
session:
|
|
59
|
-
|
|
60
|
-
|
|
43
|
+
assemblyName: asmName,
|
|
44
|
+
session: s,
|
|
45
|
+
signal,
|
|
46
|
+
statusCallback: slot(),
|
|
47
|
+
})
|
|
48
|
+
: Promise.resolve(''),
|
|
49
|
+
upDownBp > 0
|
|
50
|
+
? fetchSeq({
|
|
61
51
|
start: end,
|
|
62
|
-
end:
|
|
52
|
+
end: end + upDownBp,
|
|
63
53
|
refName,
|
|
64
|
-
assemblyName,
|
|
65
|
-
session:
|
|
66
|
-
|
|
67
|
-
|
|
68
|
-
|
|
69
|
-
|
|
70
|
-
|
|
71
|
-
|
|
72
|
-
|
|
73
|
-
|
|
74
|
-
|
|
75
|
-
setError(err);
|
|
76
|
-
}
|
|
77
|
-
finally {
|
|
78
|
-
setLoading(false);
|
|
79
|
-
}
|
|
80
|
-
})();
|
|
81
|
-
}, [key, session]);
|
|
82
|
-
return {
|
|
83
|
-
sequence,
|
|
84
|
-
loading,
|
|
85
|
-
error,
|
|
86
|
-
};
|
|
54
|
+
assemblyName: asmName,
|
|
55
|
+
session: s,
|
|
56
|
+
signal,
|
|
57
|
+
statusCallback: slot(),
|
|
58
|
+
})
|
|
59
|
+
: Promise.resolve(''),
|
|
60
|
+
]);
|
|
61
|
+
return { seq, upstream, downstream };
|
|
62
|
+
}
|
|
63
|
+
: null);
|
|
64
|
+
return { sequence, loading, error, status };
|
|
87
65
|
}
|
|
@@ -0,0 +1,55 @@
|
|
|
1
|
+
import type { RpcStatus, StatusCallback } from './progress.ts';
|
|
2
|
+
export type FetchKey = string | readonly unknown[] | null | undefined | false;
|
|
3
|
+
type FetchingKey<Key> = Exclude<Key, null | undefined | false>;
|
|
4
|
+
/**
|
|
5
|
+
* The fetcher's parameter list, derived from the key. An array key is spread
|
|
6
|
+
* into the parameters, so a tuple key gives the fetcher one typed parameter per
|
|
7
|
+
* element (`MafSequenceWidget` destructures its key that way, to reuse the
|
|
8
|
+
* narrowing the null-key ternary already did); a string key arrives as the
|
|
9
|
+
* single argument (`useGenomesData`). Most fetchers close over what they need
|
|
10
|
+
* and declare no parameters at all, which stays assignable either way.
|
|
11
|
+
*
|
|
12
|
+
* A signal and a status callback follow the key arguments. The signal is
|
|
13
|
+
* created per fetch and aborted when the key changes or the component unmounts,
|
|
14
|
+
* so a fetcher that forwards it to an RPC cancels the worker instead of leaving
|
|
15
|
+
* it grinding on an answer nobody is waiting for. The callback is what the RPC's
|
|
16
|
+
* own progress comes back through, and it surfaces on the hook's `status` — a
|
|
17
|
+
* dialog that forwards both gets "Downloading features 42%" and a cancel that
|
|
18
|
+
* works, instead of a bare spinner over an uninterruptible whole-chromosome
|
|
19
|
+
* read. Fetchers that take neither are unaffected.
|
|
20
|
+
*/
|
|
21
|
+
type FetcherArgs<Key> = FetchingKey<Key> extends readonly unknown[] ? [...FetchingKey<Key>, AbortSignal, StatusCallback] : [FetchingKey<Key>, AbortSignal, StatusCallback];
|
|
22
|
+
interface FetchState<Data> {
|
|
23
|
+
data: Data | undefined;
|
|
24
|
+
error: unknown;
|
|
25
|
+
isLoading: boolean;
|
|
26
|
+
}
|
|
27
|
+
interface UseFetchOptions<Data> {
|
|
28
|
+
onError?: (error: unknown) => void;
|
|
29
|
+
onSuccess?: (data: Data) => void;
|
|
30
|
+
}
|
|
31
|
+
interface UseFetchResponse<Data> extends FetchState<Data> {
|
|
32
|
+
/**
|
|
33
|
+
* Trigger a refetch. Returns nothing: the result arrives through
|
|
34
|
+
* `data`/`error`/`isLoading` like the initial fetch, and a promise here could
|
|
35
|
+
* only resolve before the refetch it schedules had run.
|
|
36
|
+
*/
|
|
37
|
+
mutate: () => void;
|
|
38
|
+
isValidating: boolean;
|
|
39
|
+
/**
|
|
40
|
+
* Latest progress the in-flight fetcher reported through its status callback,
|
|
41
|
+
* or undefined when it reported none or the fetch has settled. Render it with
|
|
42
|
+
* `statusProgressLabel` (and `statusFraction` for a bar); a fetcher that never
|
|
43
|
+
* calls its callback leaves this undefined and the consumer shows whatever it
|
|
44
|
+
* showed before.
|
|
45
|
+
*/
|
|
46
|
+
status: RpcStatus | undefined;
|
|
47
|
+
}
|
|
48
|
+
/**
|
|
49
|
+
* Revalidate every mounted `useFetch` on this key. Synchronous for the same
|
|
50
|
+
* reason the per-hook `mutate` is: it schedules the refetches, and each hook
|
|
51
|
+
* reports its own result through the state it already exposes.
|
|
52
|
+
*/
|
|
53
|
+
export declare function mutate(key: FetchKey): void;
|
|
54
|
+
export declare function useFetch<Data = unknown, Key extends FetchKey = FetchKey>(key: Key, fetcher: ((...args: FetcherArgs<Key>) => Promise<Data>) | null, options?: UseFetchOptions<Data>): UseFetchResponse<Data>;
|
|
55
|
+
export {};
|
|
@@ -0,0 +1,197 @@
|
|
|
1
|
+
import { useCallback, useEffect, useRef, useState } from 'react';
|
|
2
|
+
import { createStatusWindow } from './progress.js';
|
|
3
|
+
// The whole key as the "don't fetch" sentinel: `cond && [...]`, `cond ? [...] :
|
|
4
|
+
// null`. `false` belongs here and NOT in the element check below, which is what
|
|
5
|
+
// this used to share with it.
|
|
6
|
+
const isNoKey = (k) => k === null || k === undefined || k === false;
|
|
7
|
+
// An element that has not resolved yet — an offset still being computed, an
|
|
8
|
+
// assembly still loading. **`false` is not one of them**: it is a resolved
|
|
9
|
+
// boolean, and a caller with a `false`-valued setting in its key meant to fetch
|
|
10
|
+
// under that setting. Sharing one predicate with the sentinel above made every
|
|
11
|
+
// such key unfetchable, which the MAF sequence widget shipped — its
|
|
12
|
+
// `includeInsertions` defaults to `false`, so the widget sat on its loading
|
|
13
|
+
// animation forever and issued no RPC at all. `SaveTrackData` hit the same
|
|
14
|
+
// thing and encoded its boolean as a string rather than fixing it here.
|
|
15
|
+
const isUnresolved = (k) => k === null || k === undefined;
|
|
16
|
+
function serializeKey(key) {
|
|
17
|
+
return isNoKey(key) || (Array.isArray(key) && key.some(isUnresolved))
|
|
18
|
+
? null
|
|
19
|
+
: JSON.stringify(key);
|
|
20
|
+
}
|
|
21
|
+
// Cross-component refetch coordination, keyed by serialized key. Holds only
|
|
22
|
+
// refetch callbacks (never data), so there is no global cache to go stale —
|
|
23
|
+
// this is the one SWR feature we relied on: mutate(key) revalidates every
|
|
24
|
+
// mounted useFetch sharing that key.
|
|
25
|
+
const listeners = new Map();
|
|
26
|
+
/**
|
|
27
|
+
* Revalidate every mounted `useFetch` on this key. Synchronous for the same
|
|
28
|
+
* reason the per-hook `mutate` is: it schedules the refetches, and each hook
|
|
29
|
+
* reports its own result through the state it already exposes.
|
|
30
|
+
*/
|
|
31
|
+
export function mutate(key) {
|
|
32
|
+
const serialized = serializeKey(key);
|
|
33
|
+
if (serialized) {
|
|
34
|
+
for (const refetch of listeners.get(serialized) ?? []) {
|
|
35
|
+
refetch();
|
|
36
|
+
}
|
|
37
|
+
}
|
|
38
|
+
}
|
|
39
|
+
export function useFetch(key, fetcher, options = {}) {
|
|
40
|
+
const serialized = serializeKey(key);
|
|
41
|
+
// A null fetcher is the second way to say "don't fetch", so its nullness is a
|
|
42
|
+
// fetch input exactly like the key is — the effect below has to re-run when it
|
|
43
|
+
// flips. Only the boolean can go in the dependency list: the fetcher itself is
|
|
44
|
+
// usually an inline closure, so depending on its identity would refetch every
|
|
45
|
+
// render. Tracked separately from the key because the two are independent —
|
|
46
|
+
// gating on the key alone leaves a `fetcher` that resolves from null to a real
|
|
47
|
+
// function (an adapter/config arriving late) permanently stuck not fetching.
|
|
48
|
+
const hasFetcher = fetcher !== null;
|
|
49
|
+
const [state, setState] = useState(() => ({
|
|
50
|
+
data: undefined,
|
|
51
|
+
error: undefined,
|
|
52
|
+
// seeded from the key rather than starting false: the effect below runs
|
|
53
|
+
// after the first paint, so a false seed showed the resolved-and-empty state
|
|
54
|
+
// for a frame before the spinner (an empty attribute table, an empty list)
|
|
55
|
+
isLoading: serialized !== null && hasFetcher,
|
|
56
|
+
}));
|
|
57
|
+
// bumped to force a refetch (local mutate() or a cross-component mutate(key))
|
|
58
|
+
const [nonce, setNonce] = useState(0);
|
|
59
|
+
// separate from `state` because it moves on its own cadence: the RPC status
|
|
60
|
+
// stream ticks throughout one fetch, while data/error/isLoading move once
|
|
61
|
+
const [status, setStatus] = useState(undefined);
|
|
62
|
+
// refs let the fetch effect depend only on the serialized key + nonce without
|
|
63
|
+
// re-running when the (often inline) fetcher/options/key identities change
|
|
64
|
+
const optionsRef = useRef(options);
|
|
65
|
+
optionsRef.current = options;
|
|
66
|
+
const fetcherRef = useRef(fetcher);
|
|
67
|
+
fetcherRef.current = fetcher;
|
|
68
|
+
const keyRef = useRef(key);
|
|
69
|
+
keyRef.current = key;
|
|
70
|
+
// the key the last fetch ran under, to tell a mutate()-driven refetch from a
|
|
71
|
+
// key change — see the setState below
|
|
72
|
+
const fetchedKeyRef = useRef(null);
|
|
73
|
+
useEffect(() => {
|
|
74
|
+
const key = keyRef.current;
|
|
75
|
+
const fetcher = fetcherRef.current;
|
|
76
|
+
if (serialized === null || !fetcher) {
|
|
77
|
+
// when the key becomes null, callers see undefined data again rather
|
|
78
|
+
// than the prior fetch's result
|
|
79
|
+
fetchedKeyRef.current = null;
|
|
80
|
+
setState({ data: undefined, error: undefined, isLoading: false });
|
|
81
|
+
// and the same for the progress, which otherwise sticks: a key going nil
|
|
82
|
+
// *during* a fetch runs this branch's cleanup first, so the `alive` guard
|
|
83
|
+
// on the settle below has already closed and nothing else clears it
|
|
84
|
+
setStatus(undefined);
|
|
85
|
+
return undefined;
|
|
86
|
+
}
|
|
87
|
+
else {
|
|
88
|
+
let alive = true;
|
|
89
|
+
// `alive` is about this effect run; `settled` is about this fetch. They
|
|
90
|
+
// differ for exactly one thing, the status stream below: an RPC resolves
|
|
91
|
+
// its status channel asynchronously, so a status can arrive after the
|
|
92
|
+
// fetch it describes has resolved — and without a second term it lands on
|
|
93
|
+
// top of the clear and sticks. (The trailing write queued *before* the
|
|
94
|
+
// fetch resolved is a different case, and the stream's own `clear` drops
|
|
95
|
+
// that one.)
|
|
96
|
+
let settled = false;
|
|
97
|
+
const controller = new AbortController();
|
|
98
|
+
// A refetch under the same key — mutate(), or the cross-component
|
|
99
|
+
// mutate(key) — is the same question asked again, so what is on screen is
|
|
100
|
+
// a stale answer to it rather than an answer to something else: leave it
|
|
101
|
+
// up and let `isLoading` say it is being rechecked. A key *change* still
|
|
102
|
+
// clears, because the old data describes a different question.
|
|
103
|
+
//
|
|
104
|
+
// Blanking on every refetch is what made the desktop start screen flash
|
|
105
|
+
// "No sessions available" after each rename, delete, or cancelled dialog.
|
|
106
|
+
// Consumers that want the old view gone during a revalidate already have
|
|
107
|
+
// it: they gate on `isLoading`, which is unchanged.
|
|
108
|
+
const sameKey = fetchedKeyRef.current === serialized;
|
|
109
|
+
fetchedKeyRef.current = serialized;
|
|
110
|
+
setState(prev => ({
|
|
111
|
+
data: sameKey ? prev.data : undefined,
|
|
112
|
+
error: undefined,
|
|
113
|
+
isLoading: true,
|
|
114
|
+
}));
|
|
115
|
+
// the previous fetch's last progress describes work that is over
|
|
116
|
+
setStatus(undefined);
|
|
117
|
+
// The runtime counterpart of FetcherArgs: an array key becomes one
|
|
118
|
+
// argument per element, anything else a single argument, then the stop
|
|
119
|
+
// signal and the status callback. A conditional type over an unresolved
|
|
120
|
+
// `Key` can't be discharged
|
|
121
|
+
// inside the function body, so the parameter list is erased for this one
|
|
122
|
+
// call — callers still get the precise arity, and the looseness stops
|
|
123
|
+
// here.
|
|
124
|
+
const keyArgs = Array.isArray(key) ? key : [key];
|
|
125
|
+
// guarded and throttled for the same reason every other owner of a
|
|
126
|
+
// progress stream is: an RPC emits ~40 of these a second, and each one
|
|
127
|
+
// re-renders the dialog holding this hook
|
|
128
|
+
// one fetch is one stream, so the window is this effect run's
|
|
129
|
+
// the one writer, so the settle below clears through the same guard its
|
|
130
|
+
// statuses pass
|
|
131
|
+
const statusWindow = createStatusWindow(status => {
|
|
132
|
+
if (alive) {
|
|
133
|
+
setStatus(status);
|
|
134
|
+
}
|
|
135
|
+
});
|
|
136
|
+
const { statusCallback, clear: clearStatus } = statusWindow.open({
|
|
137
|
+
isCurrent: () => alive && !settled,
|
|
138
|
+
});
|
|
139
|
+
const args = [...keyArgs, controller.signal, statusCallback];
|
|
140
|
+
const call = fetcher;
|
|
141
|
+
Promise.resolve()
|
|
142
|
+
.then(() => call(...args))
|
|
143
|
+
.then(data => {
|
|
144
|
+
if (alive) {
|
|
145
|
+
setState({ data, error: undefined, isLoading: false });
|
|
146
|
+
optionsRef.current.onSuccess?.(data);
|
|
147
|
+
}
|
|
148
|
+
})
|
|
149
|
+
.catch((error) => {
|
|
150
|
+
if (alive) {
|
|
151
|
+
setState({ data: undefined, error, isLoading: false });
|
|
152
|
+
optionsRef.current.onError?.(error);
|
|
153
|
+
}
|
|
154
|
+
})
|
|
155
|
+
.finally(() => {
|
|
156
|
+
// however it settled, the progress it reported describes work that is
|
|
157
|
+
// over
|
|
158
|
+
settled = true;
|
|
159
|
+
clearStatus();
|
|
160
|
+
});
|
|
161
|
+
return () => {
|
|
162
|
+
alive = false;
|
|
163
|
+
// the signal's lifetime is this fetch's. An abort rejection lands in the
|
|
164
|
+
// catch above with alive already false, so it never surfaces as an error
|
|
165
|
+
controller.abort();
|
|
166
|
+
// and the window's lifetime is too: `alive` already makes a queued
|
|
167
|
+
// trailing write a no-op, but the timer behind it would otherwise stand
|
|
168
|
+
// for up to a window past unmount
|
|
169
|
+
statusWindow.reset();
|
|
170
|
+
};
|
|
171
|
+
}
|
|
172
|
+
}, [serialized, hasFetcher, nonce]);
|
|
173
|
+
// register this instance so a cross-component mutate(key) can refetch it
|
|
174
|
+
useEffect(() => {
|
|
175
|
+
if (serialized === null) {
|
|
176
|
+
return undefined;
|
|
177
|
+
}
|
|
178
|
+
else {
|
|
179
|
+
const refetch = () => {
|
|
180
|
+
setNonce(n => n + 1);
|
|
181
|
+
};
|
|
182
|
+
const set = listeners.get(serialized) ?? new Set();
|
|
183
|
+
set.add(refetch);
|
|
184
|
+
listeners.set(serialized, set);
|
|
185
|
+
return () => {
|
|
186
|
+
set.delete(refetch);
|
|
187
|
+
if (set.size === 0) {
|
|
188
|
+
listeners.delete(serialized);
|
|
189
|
+
}
|
|
190
|
+
};
|
|
191
|
+
}
|
|
192
|
+
}, [serialized]);
|
|
193
|
+
const mutate = useCallback(() => {
|
|
194
|
+
setNonce(n => n + 1);
|
|
195
|
+
}, []);
|
|
196
|
+
return { ...state, mutate, isValidating: state.isLoading, status };
|
|
197
|
+
}
|
|
@@ -0,0 +1,16 @@
|
|
|
1
|
+
/**
|
|
2
|
+
* The plugin store listing. Shared by every surface that installs plugins (the
|
|
3
|
+
* in-session plugin store widget, Desktop's global plugins dialog) so they read
|
|
4
|
+
* the same manifest version and get the same integrity hashes and compatibility
|
|
5
|
+
* ranges — a second copy of this fetch is how one of them silently ends up on
|
|
6
|
+
* the unhashed v1 list.
|
|
7
|
+
*
|
|
8
|
+
* Through `fetchPlugins`, which memoizes its request, rather than fetching the
|
|
9
|
+
* url directly: `useFetch` holds no data cache, so every open of the store
|
|
10
|
+
* widget was a fresh round trip beside whatever the boot path had already
|
|
11
|
+
* asked for.
|
|
12
|
+
*/
|
|
13
|
+
export declare function useFetchPlugins(): {
|
|
14
|
+
plugins: import("./index.ts").JBrowsePlugin[] | undefined;
|
|
15
|
+
error: unknown;
|
|
16
|
+
};
|
|
@@ -0,0 +1,18 @@
|
|
|
1
|
+
import { fetchPlugins } from '../checkPlugins.js';
|
|
2
|
+
import { useFetch } from './useFetch.js';
|
|
3
|
+
/**
|
|
4
|
+
* The plugin store listing. Shared by every surface that installs plugins (the
|
|
5
|
+
* in-session plugin store widget, Desktop's global plugins dialog) so they read
|
|
6
|
+
* the same manifest version and get the same integrity hashes and compatibility
|
|
7
|
+
* ranges — a second copy of this fetch is how one of them silently ends up on
|
|
8
|
+
* the unhashed v1 list.
|
|
9
|
+
*
|
|
10
|
+
* Through `fetchPlugins`, which memoizes its request, rather than fetching the
|
|
11
|
+
* url directly: `useFetch` holds no data cache, so every open of the store
|
|
12
|
+
* widget was a fresh round trip beside whatever the boot path had already
|
|
13
|
+
* asked for.
|
|
14
|
+
*/
|
|
15
|
+
export function useFetchPlugins() {
|
|
16
|
+
const { data, error } = useFetch('jbrowse-plugin-store-v2', fetchPlugins);
|
|
17
|
+
return { plugins: data?.plugins, error };
|
|
18
|
+
}
|
package/esm/util/useMeasure.d.ts
CHANGED
|
@@ -1,4 +1,14 @@
|
|
|
1
|
-
|
|
1
|
+
/**
|
|
2
|
+
* Element size, via ResizeObserver.
|
|
3
|
+
*
|
|
4
|
+
* `track` names the axes the caller actually uses, and it is a performance knob
|
|
5
|
+
* as much as an API one: the observer fires for a change on *either* axis, so a
|
|
6
|
+
* width-only caller re-rendered every time its content grew taller. That is the
|
|
7
|
+
* common case in a view container, whose height follows its tracks. Naming the
|
|
8
|
+
* axis lets those updates be dropped instead. The unnamed axis is reported as
|
|
9
|
+
* `undefined` rather than a stale number, so nothing can quietly read it.
|
|
10
|
+
*/
|
|
11
|
+
export default function useMeasure(track?: 'both' | 'width' | 'height'): readonly [import("react").RefObject<HTMLDivElement | null>, {
|
|
2
12
|
width?: number;
|
|
3
13
|
height?: number;
|
|
4
14
|
}];
|