@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
package/esm/PluginLoader.d.ts
CHANGED
|
@@ -1,64 +1,75 @@
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1
1
|
import type { PluginConstructor } from './Plugin.ts';
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2
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-
|
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3
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-
umdLoc: {
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4
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-
uri: string;
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5
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-
baseUri?: string;
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6
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-
};
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7
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-
name: string;
|
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8
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-
}
|
|
9
|
-
export interface UMDUrlPluginDefinition {
|
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10
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-
umdUrl: string;
|
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11
|
-
name: string;
|
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12
|
-
}
|
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13
|
-
export interface LegacyUMDPluginDefinition {
|
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14
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-
url: string;
|
|
15
|
-
name: string;
|
|
16
|
-
}
|
|
17
|
-
type UMDPluginDefinition = UMDLocPluginDefinition | UMDUrlPluginDefinition;
|
|
18
|
-
export declare function isUMDPluginDefinition(def: PluginDefinition): def is UMDPluginDefinition | LegacyUMDPluginDefinition;
|
|
19
|
-
export interface ESMLocPluginDefinition {
|
|
20
|
-
esmLoc: {
|
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21
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-
uri: string;
|
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22
|
-
baseUri?: string;
|
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23
|
-
};
|
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24
|
-
}
|
|
25
|
-
export interface ESMUrlPluginDefinition {
|
|
26
|
-
esmUrl: string;
|
|
27
|
-
}
|
|
28
|
-
export type ESMPluginDefinition = ESMLocPluginDefinition | ESMUrlPluginDefinition;
|
|
29
|
-
export declare function isESMPluginDefinition(def: PluginDefinition): def is ESMPluginDefinition;
|
|
30
|
-
export interface CJSPluginDefinition {
|
|
31
|
-
cjsUrl: string;
|
|
32
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-
}
|
|
33
|
-
export declare function isCJSPluginDefinition(def: PluginDefinition): def is CJSPluginDefinition;
|
|
34
|
-
export type PluginDefinition = UMDUrlPluginDefinition | UMDLocPluginDefinition | LegacyUMDPluginDefinition | ESMLocPluginDefinition | ESMUrlPluginDefinition | CJSPluginDefinition;
|
|
2
|
+
import type { ESMPluginDefinition, LegacyUMDPluginDefinition, PluginDefinition, UMDPluginDefinition } from './pluginDefinitions.ts';
|
|
35
3
|
export interface PluginRecord {
|
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36
4
|
plugin: PluginConstructor;
|
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37
5
|
definition: PluginDefinition;
|
|
38
6
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}
|
|
7
|
+
export type ReExportRegistryLoader = () => Promise<{
|
|
8
|
+
default: Record<string, unknown>;
|
|
9
|
+
}>;
|
|
39
10
|
export interface LoadedPlugin {
|
|
40
11
|
default: PluginConstructor;
|
|
41
12
|
}
|
|
42
|
-
|
|
43
|
-
export
|
|
13
|
+
/** A definition that could not be loaded, kept with the reason it failed */
|
|
14
|
+
export interface PluginLoadFailure {
|
|
15
|
+
definition: PluginDefinition;
|
|
16
|
+
error: unknown;
|
|
17
|
+
}
|
|
18
|
+
export declare function workerScriptLoadMessage(scriptUrl: string, error: unknown): string;
|
|
19
|
+
/**
|
|
20
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+
* The registry has to be published before a plugin bundle runs, but not before
|
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|
+
* it downloads, so each bundle is preloaded while the registry is fetched.
|
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22
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+
* Skipped under the cache-buster, whose query string differs per request.
|
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23
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+
*
|
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24
|
+
* Exported for a worker told its plugins ahead of its boot configuration.
|
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25
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+
*/
|
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26
|
+
export declare function preloadUMDBundles(defs: PluginDefinition[], baseUri?: string): void;
|
|
44
27
|
export default class PluginLoader {
|
|
45
28
|
definitions: PluginDefinition[];
|
|
46
29
|
fetchESM?: (url: string) => Promise<LoadedPlugin>;
|
|
47
|
-
fetchCJS?: (url: string) => Promise<LoadedPlugin>;
|
|
48
30
|
constructor(defs?: PluginDefinition[], args?: {
|
|
49
31
|
fetchESM?: (url: string) => Promise<LoadedPlugin>;
|
|
50
|
-
fetchCJS?: (url: string) => Promise<LoadedPlugin>;
|
|
51
32
|
});
|
|
52
|
-
loadCJSPlugin(def: CJSPluginDefinition, baseUri?: string): Promise<LoadedPlugin>;
|
|
53
33
|
loadESMPlugin(def: ESMPluginDefinition, baseUri?: string): Promise<LoadedPlugin>;
|
|
54
34
|
loadUMDPlugin(def: UMDPluginDefinition | LegacyUMDPluginDefinition, baseUri?: string): Promise<{
|
|
55
35
|
default: PluginConstructor;
|
|
56
36
|
}>;
|
|
57
37
|
loadPlugin(def: PluginDefinition, baseUri?: string): Promise<PluginConstructor>;
|
|
58
|
-
|
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59
|
-
|
|
60
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-
|
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61
|
-
|
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62
|
-
|
|
38
|
+
private reExports;
|
|
39
|
+
/**
|
|
40
|
+
* Ask for the runtime ABI (`JBrowseExports`) to be published on `target`
|
|
41
|
+
* before any plugin bundle is evaluated. Records the target and the loader;
|
|
42
|
+
* `loadSettled` fetches the registry, a ~126 KB gzipped module only a runtime
|
|
43
|
+
* plugin can use (see `ReExports/registry.ts` for why it cannot shrink).
|
|
44
|
+
*
|
|
45
|
+
* `registry` is the product's generated map — `reExports.generated.ts` on
|
|
46
|
+
* the main thread, `workerReExports.generated.ts` in its worker — which
|
|
47
|
+
* serves every `@jbrowse` package the product bundles. The caller names it
|
|
48
|
+
* because the registry serves this module: an `import()` of it from here is
|
|
49
|
+
* a cycle rolldown keeps in any host bundling this file, whether or not
|
|
50
|
+
* anything loads a plugin (EAGER_BUNDLE.md §3).
|
|
51
|
+
*/
|
|
52
|
+
installGlobalReExports(target: WindowOrWorkerGlobalScope, registry: ReExportRegistryLoader): this;
|
|
53
|
+
private publishReExports;
|
|
54
|
+
/**
|
|
55
|
+
* Loads every definition and separates the ones that worked from the ones
|
|
56
|
+
* that didn't, instead of failing the batch on the first error.
|
|
57
|
+
*
|
|
58
|
+
* A remote config names its plugins at urls nobody re-checks — a store path
|
|
59
|
+
* that stops being republished, a bundle that needs a newer host than the one
|
|
60
|
+
* reading the config — and `load`'s all-or-nothing contract turns any of that
|
|
61
|
+
* into a dead app rather than a missing feature. That is the widest blast
|
|
62
|
+
* radius left in config loading: an unknown track/adapter/display type is
|
|
63
|
+
* already tolerated (the track is simply not usable), so the plugin url was
|
|
64
|
+
* the only field in a config that could still take a whole session down.
|
|
65
|
+
*
|
|
66
|
+
* Callers that can degrade (the apps) use this and report the failures;
|
|
67
|
+
* callers that cannot (the RPC worker, where a half-loaded plugin set would
|
|
68
|
+
* fail renders with a much worse message) keep using `load`.
|
|
69
|
+
*/
|
|
70
|
+
loadSettled(baseUri?: string): Promise<{
|
|
71
|
+
records: PluginRecord[];
|
|
72
|
+
failures: PluginLoadFailure[];
|
|
73
|
+
}>;
|
|
74
|
+
load(baseUri?: string): Promise<PluginRecord[]>;
|
|
63
75
|
}
|
|
64
|
-
export {};
|
package/esm/PluginLoader.js
CHANGED
|
@@ -1,21 +1,50 @@
|
|
|
1
|
-
import
|
|
2
|
-
import
|
|
3
|
-
import {
|
|
4
|
-
|
|
5
|
-
|
|
6
|
-
|
|
7
|
-
|
|
8
|
-
|
|
1
|
+
import { enableContractReports } from '@jbrowse/render-core/contractReports';
|
|
2
|
+
import { loudOnMissingModule, setReExportRegistry, } from './ReExports/registry.js';
|
|
3
|
+
import { isESMPluginDefinition, isUMDPluginDefinition, maybePluginUrl, pluginDescriptionString, pluginLabel, } from './pluginDefinitions.js';
|
|
4
|
+
import { isWebWorker } from './util/isWebWorker.js';
|
|
5
|
+
/**
|
|
6
|
+
* A definition names exactly one loader. More than one is malformed — no real
|
|
7
|
+
* config declares a plugin twice — and it is the shape that lets "the url we
|
|
8
|
+
* vetted" and "the url we run" drift apart, so refuse it rather than pick a
|
|
9
|
+
* winner. That keeps them the same string by construction, instead of by every
|
|
10
|
+
* url-based inspection of a definition remembering to match loadPlugin's order.
|
|
11
|
+
*/
|
|
12
|
+
function assertSingleKind(def) {
|
|
13
|
+
const kinds = [
|
|
14
|
+
isESMPluginDefinition(def) ? 'ESM' : undefined,
|
|
15
|
+
isUMDPluginDefinition(def) ? 'UMD' : undefined,
|
|
16
|
+
].filter(kind => kind !== undefined);
|
|
17
|
+
if (kinds.length > 1) {
|
|
18
|
+
throw new Error(`Plugin definition names more than one plugin type (${kinds.join(', ')}), refusing to load: ${JSON.stringify(def)}`);
|
|
19
|
+
}
|
|
9
20
|
}
|
|
10
|
-
|
|
11
|
-
|
|
12
|
-
|
|
21
|
+
/**
|
|
22
|
+
* A `cjsUrl` definition loaded by writing the bundle to a temp file and
|
|
23
|
+
* `require`ing it in Electron's renderer, the one loader that needed Node. That
|
|
24
|
+
* renderer runs UMD and ESM, and a plugin reaching the main process does it
|
|
25
|
+
* through `window.require('electron')` whatever format it ships in, so the
|
|
26
|
+
* format bought nothing its two peers do not. Name the successor rather than
|
|
27
|
+
* letting the definition fall through to "could not determine plugin type",
|
|
28
|
+
* which reads as a malformed config.
|
|
29
|
+
*/
|
|
30
|
+
function assertRetiredKinds(def) {
|
|
31
|
+
if ('cjsUrl' in def) {
|
|
32
|
+
throw new Error(`CJS plugins are no longer loaded (${String(def.cjsUrl)}). Publish the plugin as UMD or ESM and name it with umdUrl or esmUrl.`);
|
|
33
|
+
}
|
|
13
34
|
}
|
|
14
|
-
function promisifiedLoadScript(src) {
|
|
35
|
+
function promisifiedLoadScript(src, integrity) {
|
|
15
36
|
return new Promise((resolve, reject) => {
|
|
16
37
|
const script = document.createElement('script');
|
|
17
38
|
script.type = 'text/javascript';
|
|
18
39
|
script.async = true;
|
|
40
|
+
// Subresource integrity guarantees the fetched bytes match the hash the
|
|
41
|
+
// plugin store published, so a tampered or swapped artifact fails to load.
|
|
42
|
+
// crossOrigin is required for the browser to enforce integrity on a
|
|
43
|
+
// cross-origin script.
|
|
44
|
+
if (integrity) {
|
|
45
|
+
script.integrity = integrity;
|
|
46
|
+
script.crossOrigin = 'anonymous';
|
|
47
|
+
}
|
|
19
48
|
script.src = src;
|
|
20
49
|
script.onload = () => {
|
|
21
50
|
resolve(script.src);
|
|
@@ -26,111 +55,205 @@ function promisifiedLoadScript(src) {
|
|
|
26
55
|
document.head.append(script);
|
|
27
56
|
});
|
|
28
57
|
}
|
|
29
|
-
|
|
30
|
-
|
|
31
|
-
return promisifiedLoadScript(scriptUrl);
|
|
32
|
-
}
|
|
33
|
-
if (globalThis.importScripts) {
|
|
34
|
-
await globalThis.importScripts(scriptUrl);
|
|
35
|
-
return;
|
|
36
|
-
}
|
|
37
|
-
throw new Error('cannot figure out how to load external JS scripts in this environment');
|
|
58
|
+
function hasImportScripts(scope) {
|
|
59
|
+
return 'importScripts' in scope;
|
|
38
60
|
}
|
|
39
|
-
|
|
40
|
-
|
|
61
|
+
// A *module* worker has importScripts on its global but throws from it — the
|
|
62
|
+
// spec forbids it there, and the browser says so ("Module scripts don't support
|
|
63
|
+
// importScripts"). That is the whole failure for a UMD plugin in a bundler
|
|
64
|
+
// configured for module workers (Vite's `worker.format: 'es'`), and it reads as
|
|
65
|
+
// a broken plugin unless named. Every other throw is the script's own — a 404,
|
|
66
|
+
// or a bundle that dereferences `window` in a realm that has none — and the
|
|
67
|
+
// script's words are the diagnosis, so they are kept rather than replaced.
|
|
68
|
+
export function workerScriptLoadMessage(scriptUrl, error) {
|
|
69
|
+
const detail = error instanceof Error ? error.message : String(error);
|
|
70
|
+
return /module script/i.test(detail)
|
|
71
|
+
? `Failed to load ${scriptUrl} in the worker. A UMD plugin is loaded there via importScripts, which module workers do not support — either build the worker as a classic worker, or use a plugin published as ESM.`
|
|
72
|
+
: `Failed to load ${scriptUrl} in the worker: ${detail}`;
|
|
41
73
|
}
|
|
42
|
-
|
|
43
|
-
|
|
44
|
-
|
|
74
|
+
const workerPrefetches = new Map();
|
|
75
|
+
/**
|
|
76
|
+
* `importScripts` blocks until its file arrives, so a worker loading its
|
|
77
|
+
* plugins with it waited one round trip per plugin, in a row. Fetching them all
|
|
78
|
+
* first makes each `importScripts` a cache read — provided the fetch is the
|
|
79
|
+
* request `importScripts` makes: no-cors, with credentials. Chrome and Firefox
|
|
80
|
+
* both re-download for any other mode (probe-worker-script-cache.ts).
|
|
81
|
+
*/
|
|
82
|
+
function prefetchWorkerScript(url) {
|
|
83
|
+
if (!workerPrefetches.has(url)) {
|
|
84
|
+
workerPrefetches.set(url, fetch(url, { mode: 'no-cors', credentials: 'include' })
|
|
85
|
+
.then(r => r.arrayBuffer())
|
|
86
|
+
.then(() => { }, () => { }));
|
|
45
87
|
}
|
|
46
|
-
|
|
47
|
-
|
|
48
|
-
|
|
88
|
+
}
|
|
89
|
+
async function loadScript(scriptUrl, integrity) {
|
|
90
|
+
const scope = globalThis;
|
|
91
|
+
if (!isWebWorker()) {
|
|
92
|
+
return promisifiedLoadScript(scriptUrl, integrity);
|
|
49
93
|
}
|
|
50
|
-
else if (
|
|
51
|
-
|
|
94
|
+
else if (hasImportScripts(scope)) {
|
|
95
|
+
await workerPrefetches.get(scriptUrl);
|
|
96
|
+
try {
|
|
97
|
+
scope.importScripts(scriptUrl);
|
|
98
|
+
}
|
|
99
|
+
catch (error) {
|
|
100
|
+
throw new Error(workerScriptLoadMessage(scriptUrl, error), {
|
|
101
|
+
cause: error,
|
|
102
|
+
});
|
|
103
|
+
}
|
|
104
|
+
return;
|
|
52
105
|
}
|
|
53
106
|
else {
|
|
54
|
-
|
|
107
|
+
throw new Error('cannot figure out how to load external JS scripts in this environment');
|
|
55
108
|
}
|
|
56
109
|
}
|
|
57
|
-
|
|
58
|
-
|
|
59
|
-
|
|
110
|
+
/**
|
|
111
|
+
* Resolve a plugin's url, refusing anything that isn't http(s).
|
|
112
|
+
*
|
|
113
|
+
* `base` is the JBrowse **instance's** own location, not the config that named
|
|
114
|
+
* the plugin — every product passes `window.location.href` (the embedded ones
|
|
115
|
+
* let their host override it, the RPC worker forwards the same value). That is
|
|
116
|
+
* deliberate rather than an oversight: a relative url means "a plugin shipped
|
|
117
|
+
* beside this index.html". A config that means "beside *me*" has the
|
|
118
|
+
* `umdLoc`/`esmLoc` forms instead, which carry their own `baseUri` — the one
|
|
119
|
+
* `addRelativeUris` stamps from the config's url when it is fetched.
|
|
120
|
+
*
|
|
121
|
+
* The rule only bites on Desktop, whose instance is a `file://` page, so a
|
|
122
|
+
* relative url resolves to a `file:` url that could never be fetched. Diagnose
|
|
123
|
+
* that in terms its author can act on: the raw scheme of a url they never wrote
|
|
124
|
+
* ("Cannot load plugins using protocol file:") named the symptom and nothing
|
|
125
|
+
* else, and the reader is usually looking at a third-party hub config.
|
|
126
|
+
*/
|
|
127
|
+
function resolvePluginUrl(spec, base) {
|
|
128
|
+
const url = new URL(spec, base);
|
|
129
|
+
if (url.protocol !== 'http:' && url.protocol !== 'https:') {
|
|
130
|
+
throw new Error(
|
|
131
|
+
// a spec with a scheme of its own resolved to exactly what it asked for,
|
|
132
|
+
// so there is nothing to explain beyond refusing it
|
|
133
|
+
/^[a-z][a-z0-9+.-]*:/i.test(spec)
|
|
134
|
+
? `Cannot load plugins using protocol "${url.protocol}"`
|
|
135
|
+
: `Cannot load plugin from relative url "${spec}": it resolves against this JBrowse instance (${base}), not against the config that named it. Give it an absolute http(s) url, or use the umdLoc/esmLoc form to resolve it against the config.`);
|
|
60
136
|
}
|
|
61
|
-
|
|
62
|
-
|
|
137
|
+
return url;
|
|
138
|
+
}
|
|
139
|
+
// A plugin served from the developer's own machine into an app built for
|
|
140
|
+
// production is the one arrangement that can only be a plugin under
|
|
141
|
+
// development: a shipped site serves its plugins from its own origin, and a
|
|
142
|
+
// developer running the app itself from source already has a development build.
|
|
143
|
+
// So it is the evidence that arms the contract channel without anything for the
|
|
144
|
+
// author to know about first — which is the whole difficulty the channel had,
|
|
145
|
+
// since the population it is written for is the one with nobody to ask. See
|
|
146
|
+
// `@jbrowse/render-core/contractReports`.
|
|
147
|
+
function armIfUnderDevelopment(def) {
|
|
148
|
+
const url = maybePluginUrl(def);
|
|
149
|
+
if (url !== undefined && servedFromThisMachine(url)) {
|
|
150
|
+
enableContractReports(`the plugin at ${url} is served from this machine`);
|
|
63
151
|
}
|
|
64
|
-
|
|
65
|
-
|
|
152
|
+
}
|
|
153
|
+
function servedFromThisMachine(url) {
|
|
154
|
+
try {
|
|
155
|
+
const { hostname, protocol } = new URL(url);
|
|
156
|
+
return ((protocol === 'http:' || protocol === 'https:') &&
|
|
157
|
+
(hostname === 'localhost' ||
|
|
158
|
+
hostname === '127.0.0.1' ||
|
|
159
|
+
hostname === '[::1]'));
|
|
66
160
|
}
|
|
67
|
-
|
|
68
|
-
|
|
161
|
+
catch {
|
|
162
|
+
// a relative url is a plugin shipped beside this index.html, which is the
|
|
163
|
+
// site's own rather than one under development
|
|
164
|
+
return false;
|
|
69
165
|
}
|
|
70
166
|
}
|
|
71
|
-
function isInWebWorker() {
|
|
72
|
-
return 'WorkerGlobalScope' in globalThis;
|
|
73
|
-
}
|
|
74
167
|
function addCacheBuster(url) {
|
|
75
|
-
if (!globalThis
|
|
168
|
+
if (!('__jbrowseCacheBuster' in globalThis)) {
|
|
76
169
|
return url;
|
|
77
170
|
}
|
|
78
171
|
const u = new URL(url);
|
|
79
172
|
u.searchParams.set('_cb', Date.now().toString());
|
|
80
173
|
return u.href;
|
|
81
174
|
}
|
|
175
|
+
function umdPluginUrl(def, baseUri) {
|
|
176
|
+
return 'url' in def
|
|
177
|
+
? resolvePluginUrl(def.url, baseUri)
|
|
178
|
+
: 'umdUrl' in def
|
|
179
|
+
? resolvePluginUrl(def.umdUrl, baseUri)
|
|
180
|
+
: resolvePluginUrl(def.umdLoc.uri, def.umdLoc.baseUri);
|
|
181
|
+
}
|
|
182
|
+
/**
|
|
183
|
+
* The registry has to be published before a plugin bundle runs, but not before
|
|
184
|
+
* it downloads, so each bundle is preloaded while the registry is fetched.
|
|
185
|
+
* Skipped under the cache-buster, whose query string differs per request.
|
|
186
|
+
*
|
|
187
|
+
* Exported for a worker told its plugins ahead of its boot configuration.
|
|
188
|
+
*/
|
|
189
|
+
export function preloadUMDBundles(defs, baseUri) {
|
|
190
|
+
if ('__jbrowseCacheBuster' in globalThis) {
|
|
191
|
+
return;
|
|
192
|
+
}
|
|
193
|
+
if (isWebWorker()) {
|
|
194
|
+
for (const def of defs) {
|
|
195
|
+
if (isUMDPluginDefinition(def)) {
|
|
196
|
+
try {
|
|
197
|
+
prefetchWorkerScript(umdPluginUrl(def, baseUri).href);
|
|
198
|
+
}
|
|
199
|
+
catch {
|
|
200
|
+
// loadPlugin reports a url it cannot resolve
|
|
201
|
+
}
|
|
202
|
+
}
|
|
203
|
+
}
|
|
204
|
+
return;
|
|
205
|
+
}
|
|
206
|
+
if (typeof document === 'undefined') {
|
|
207
|
+
return;
|
|
208
|
+
}
|
|
209
|
+
for (const def of defs) {
|
|
210
|
+
if (isUMDPluginDefinition(def)) {
|
|
211
|
+
try {
|
|
212
|
+
const link = document.createElement('link');
|
|
213
|
+
link.rel = 'preload';
|
|
214
|
+
link.as = 'script';
|
|
215
|
+
if (def.integrity) {
|
|
216
|
+
link.setAttribute('integrity', def.integrity);
|
|
217
|
+
link.setAttribute('crossorigin', 'anonymous');
|
|
218
|
+
}
|
|
219
|
+
link.href = umdPluginUrl(def, baseUri).href;
|
|
220
|
+
document.head.append(link);
|
|
221
|
+
}
|
|
222
|
+
catch {
|
|
223
|
+
// loadPlugin reports a url it cannot resolve
|
|
224
|
+
}
|
|
225
|
+
}
|
|
226
|
+
}
|
|
227
|
+
}
|
|
82
228
|
export default class PluginLoader {
|
|
83
229
|
definitions = [];
|
|
84
230
|
fetchESM;
|
|
85
|
-
fetchCJS;
|
|
86
231
|
constructor(defs = [], args) {
|
|
87
232
|
this.fetchESM = args?.fetchESM;
|
|
88
|
-
this.
|
|
89
|
-
this.definitions = JSON.parse(JSON.stringify(defs));
|
|
90
|
-
}
|
|
91
|
-
async loadCJSPlugin(def, baseUri) {
|
|
92
|
-
const parsedUrl = new URL(def.cjsUrl, baseUri);
|
|
93
|
-
if (parsedUrl.protocol !== 'http:' && parsedUrl.protocol !== 'https:') {
|
|
94
|
-
throw new Error(`Cannot load plugins using protocol "${parsedUrl.protocol}"`);
|
|
95
|
-
}
|
|
96
|
-
if (!this.fetchCJS) {
|
|
97
|
-
throw new Error('No fetchCJS callback provided');
|
|
98
|
-
}
|
|
99
|
-
return this.fetchCJS(parsedUrl.href);
|
|
233
|
+
this.definitions = structuredClone(defs);
|
|
100
234
|
}
|
|
101
235
|
async loadESMPlugin(def, baseUri) {
|
|
102
236
|
const parsedUrl = 'esmUrl' in def
|
|
103
|
-
?
|
|
104
|
-
:
|
|
105
|
-
if (parsedUrl.protocol !== 'http:' && parsedUrl.protocol !== 'https:') {
|
|
106
|
-
throw new Error(`cannot load plugins using protocol "${parsedUrl.protocol}"`);
|
|
107
|
-
}
|
|
237
|
+
? resolvePluginUrl(def.esmUrl, baseUri)
|
|
238
|
+
: resolvePluginUrl(def.esmLoc.uri, def.esmLoc.baseUri);
|
|
108
239
|
if (!this.fetchESM) {
|
|
109
240
|
throw new Error('No ESM fetcher installed');
|
|
110
241
|
}
|
|
111
242
|
const plugin = await this.fetchESM(addCacheBuster(parsedUrl.href));
|
|
243
|
+
// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
|
|
112
244
|
if (!plugin) {
|
|
113
245
|
throw new Error(`Could not load ESM plugin: ${parsedUrl}`);
|
|
114
246
|
}
|
|
115
247
|
return plugin;
|
|
116
248
|
}
|
|
117
249
|
async loadUMDPlugin(def, baseUri) {
|
|
118
|
-
const parsedUrl =
|
|
119
|
-
? new URL(def.url, baseUri)
|
|
120
|
-
: 'umdUrl' in def
|
|
121
|
-
? new URL(def.umdUrl, baseUri)
|
|
122
|
-
: new URL(def.umdLoc.uri, def.umdLoc.baseUri);
|
|
123
|
-
if (parsedUrl.protocol !== 'http:' && parsedUrl.protocol !== 'https:') {
|
|
124
|
-
throw new Error(`cannot load plugins using protocol "${parsedUrl.protocol}"`);
|
|
125
|
-
}
|
|
250
|
+
const parsedUrl = umdPluginUrl(def, baseUri);
|
|
126
251
|
const moduleName = def.name;
|
|
127
252
|
const umdName = `JBrowsePlugin${moduleName}`;
|
|
128
|
-
|
|
129
|
-
|
|
130
|
-
|
|
131
|
-
|
|
132
|
-
globalThis[umdName] = { default: Plugin };
|
|
133
|
-
}
|
|
253
|
+
// a cache buster query string would change the bytes the browser hashes for
|
|
254
|
+
// SRI, so skip it when an integrity hash is present (the url is already
|
|
255
|
+
// version-pinned and immutable, so cache-busting is unnecessary anyway)
|
|
256
|
+
await loadScript(def.integrity ? parsedUrl.href : addCacheBuster(parsedUrl.href), def.integrity);
|
|
134
257
|
const plugin = globalThis[umdName];
|
|
135
258
|
if (!plugin) {
|
|
136
259
|
throw new Error(`Failed to load UMD bundle for ${moduleName}, ${umdName} is undefined`);
|
|
@@ -138,37 +261,114 @@ export default class PluginLoader {
|
|
|
138
261
|
return plugin;
|
|
139
262
|
}
|
|
140
263
|
async loadPlugin(def, baseUri) {
|
|
264
|
+
assertRetiredKinds(def);
|
|
265
|
+
assertSingleKind(def);
|
|
266
|
+
armIfUnderDevelopment(def);
|
|
141
267
|
let plugin;
|
|
142
|
-
if (
|
|
143
|
-
plugin = await this.loadCJSPlugin(def, baseUri);
|
|
144
|
-
}
|
|
145
|
-
else if (isESMPluginDefinition(def)) {
|
|
268
|
+
if (isESMPluginDefinition(def)) {
|
|
146
269
|
plugin = await this.loadESMPlugin(def, baseUri);
|
|
147
270
|
}
|
|
148
271
|
else if (isUMDPluginDefinition(def)) {
|
|
149
272
|
plugin = await this.loadUMDPlugin(def, baseUri);
|
|
150
273
|
}
|
|
151
|
-
else if (!isElectron && isCJSPluginDefinition(def)) {
|
|
152
|
-
throw new Error(`CommonJS plugin found, but not in a NodeJS environment: ${JSON.stringify(def)}`);
|
|
153
|
-
}
|
|
154
274
|
else {
|
|
155
275
|
throw new Error(`Could not determine plugin type: ${JSON.stringify(def)}`);
|
|
156
276
|
}
|
|
277
|
+
// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
|
|
157
278
|
if (!plugin.default) {
|
|
158
279
|
throw new Error(`${pluginDescriptionString(def)} does not have a default export, cannot load`);
|
|
159
280
|
}
|
|
160
281
|
return plugin.default;
|
|
161
282
|
}
|
|
162
|
-
|
|
163
|
-
|
|
164
|
-
|
|
165
|
-
|
|
283
|
+
reExports;
|
|
284
|
+
/**
|
|
285
|
+
* Ask for the runtime ABI (`JBrowseExports`) to be published on `target`
|
|
286
|
+
* before any plugin bundle is evaluated. Records the target and the loader;
|
|
287
|
+
* `loadSettled` fetches the registry, a ~126 KB gzipped module only a runtime
|
|
288
|
+
* plugin can use (see `ReExports/registry.ts` for why it cannot shrink).
|
|
289
|
+
*
|
|
290
|
+
* `registry` is the product's generated map — `reExports.generated.ts` on
|
|
291
|
+
* the main thread, `workerReExports.generated.ts` in its worker — which
|
|
292
|
+
* serves every `@jbrowse` package the product bundles. The caller names it
|
|
293
|
+
* because the registry serves this module: an `import()` of it from here is
|
|
294
|
+
* a cycle rolldown keeps in any host bundling this file, whether or not
|
|
295
|
+
* anything loads a plugin (EAGER_BUNDLE.md §3).
|
|
296
|
+
*/
|
|
297
|
+
installGlobalReExports(target, registry) {
|
|
298
|
+
this.reExports = { target, registry };
|
|
166
299
|
return this;
|
|
167
300
|
}
|
|
168
|
-
async
|
|
169
|
-
|
|
301
|
+
async publishReExports() {
|
|
302
|
+
if (!this.reExports) {
|
|
303
|
+
return;
|
|
304
|
+
}
|
|
305
|
+
const { target, registry } = this.reExports;
|
|
306
|
+
const { default: ReExports } = await registry();
|
|
307
|
+
target.JBrowseExports =
|
|
308
|
+
loudOnMissingModule({ ...ReExports });
|
|
309
|
+
// the synchronous half: `pluginManager.jbrequire(name)` is what a CJS
|
|
310
|
+
// plugin calls, and it cannot await
|
|
311
|
+
setReExportRegistry(ReExports);
|
|
312
|
+
this.reExports = undefined;
|
|
313
|
+
}
|
|
314
|
+
/**
|
|
315
|
+
* Loads every definition and separates the ones that worked from the ones
|
|
316
|
+
* that didn't, instead of failing the batch on the first error.
|
|
317
|
+
*
|
|
318
|
+
* A remote config names its plugins at urls nobody re-checks — a store path
|
|
319
|
+
* that stops being republished, a bundle that needs a newer host than the one
|
|
320
|
+
* reading the config — and `load`'s all-or-nothing contract turns any of that
|
|
321
|
+
* into a dead app rather than a missing feature. That is the widest blast
|
|
322
|
+
* radius left in config loading: an unknown track/adapter/display type is
|
|
323
|
+
* already tolerated (the track is simply not usable), so the plugin url was
|
|
324
|
+
* the only field in a config that could still take a whole session down.
|
|
325
|
+
*
|
|
326
|
+
* Callers that can degrade (the apps) use this and report the failures;
|
|
327
|
+
* callers that cannot (the RPC worker, where a half-loaded plugin set would
|
|
328
|
+
* fail renders with a much worse message) keep using `load`.
|
|
329
|
+
*/
|
|
330
|
+
async loadSettled(baseUri) {
|
|
331
|
+
preloadUMDBundles(this.definitions, baseUri);
|
|
332
|
+
// before the first plugin script evaluates — a UMD bundle reads
|
|
333
|
+
// `JBrowseExports` off the global at module scope
|
|
334
|
+
await this.publishReExports();
|
|
335
|
+
const results = await Promise.allSettled(this.definitions.map(async (definition) => ({
|
|
170
336
|
plugin: await this.loadPlugin(definition, baseUri),
|
|
171
337
|
definition,
|
|
172
338
|
})));
|
|
339
|
+
const records = [];
|
|
340
|
+
const failures = [];
|
|
341
|
+
for (const [i, result] of results.entries()) {
|
|
342
|
+
if (result.status === 'fulfilled') {
|
|
343
|
+
records.push(result.value);
|
|
344
|
+
}
|
|
345
|
+
else {
|
|
346
|
+
failures.push({
|
|
347
|
+
definition: this.definitions[i],
|
|
348
|
+
error: result.reason,
|
|
349
|
+
});
|
|
350
|
+
}
|
|
351
|
+
}
|
|
352
|
+
return { records, failures };
|
|
353
|
+
}
|
|
354
|
+
async load(baseUri) {
|
|
355
|
+
const { records, failures } = await this.loadSettled(baseUri);
|
|
356
|
+
// rethrown by definition order rather than by which rejected first, so the
|
|
357
|
+
// error a strict caller sees doesn't depend on network timing.
|
|
358
|
+
//
|
|
359
|
+
// Named, because the RPC worker calls this: a plugin that throws while
|
|
360
|
+
// evaluating takes the whole RpcServer with it, and the bare error is
|
|
361
|
+
// whatever the bundle's module scope said — `Cannot read properties of
|
|
362
|
+
// undefined`, or the missing ABI key — with nothing saying which plugin
|
|
363
|
+
// read it. The message is carried rather than the error, since this one
|
|
364
|
+
// crosses postMessage and `serializeError` cannot clone an arbitrary
|
|
365
|
+
// `cause`.
|
|
366
|
+
const failure = failures[0];
|
|
367
|
+
if (failure) {
|
|
368
|
+
const { definition, error } = failure;
|
|
369
|
+
const detail = error instanceof Error ? error.message : String(error);
|
|
370
|
+
throw new Error(`plugin ${pluginLabel(definition)} failed: ${detail}`);
|
|
371
|
+
}
|
|
372
|
+
return records;
|
|
173
373
|
}
|
|
174
374
|
}
|