@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.
Files changed (1265) hide show
  1. package/README.md +1994 -0
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +14 -3
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +36 -23
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +10 -7
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +124 -21
  6. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.d.ts +2 -8
  7. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js +4 -4
  8. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts +1 -1
  9. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js +2 -5
  10. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.d.ts +1 -1
  11. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js +4 -4
  12. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.d.ts +12 -1
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +19 -5
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +18 -23
  16. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.d.ts +1 -1
  17. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +19 -40
  18. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +9 -6
  19. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +33 -30
  20. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.d.ts +11 -0
  21. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.js +11 -0
  22. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
  23. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
  24. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.d.ts +8 -0
  25. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.js +24 -0
  26. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
  27. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
  28. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
  29. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +19 -0
  30. package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.d.ts +4 -0
  31. package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.js +17 -0
  32. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +5 -3
  33. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +8 -6
  34. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
  35. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
  36. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +7 -2
  37. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +15 -20
  38. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.d.ts +16 -0
  39. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.js +50 -0
  40. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +0 -1
  41. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +9 -10
  42. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
  43. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
  44. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
  45. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +35 -24
  46. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
  47. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
  48. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +3 -3
  49. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
  50. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
  51. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
  52. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
  53. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
  54. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
  55. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
  56. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
  57. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
  58. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
  59. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
  60. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
  61. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
  62. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
  63. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
  64. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
  65. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
  66. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
  67. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
  68. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
  69. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
  70. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
  71. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +20 -0
  72. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
  73. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
  74. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
  75. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +62 -63
  76. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +69 -59
  77. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
  78. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
  79. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
  80. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
  81. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
  82. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
  83. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
  84. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
  85. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
  86. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
  87. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
  88. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
  89. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
  90. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
  91. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
  92. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
  93. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
  94. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
  95. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
  96. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
  97. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
  98. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
  99. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
  100. package/esm/BaseFeatureWidget/configSchema.d.ts +1 -1
  101. package/esm/BaseFeatureWidget/configSchema.js +1 -1
  102. package/esm/BaseFeatureWidget/formatDetails.d.ts +22 -0
  103. package/esm/BaseFeatureWidget/formatDetails.js +82 -0
  104. package/esm/BaseFeatureWidget/index.d.ts +4 -1
  105. package/esm/BaseFeatureWidget/index.js +2 -2
  106. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +102 -71
  107. package/esm/BaseFeatureWidget/stateModelFactory.js +162 -63
  108. package/esm/BaseFeatureWidget/types.d.ts +15 -8
  109. package/esm/BaseFeatureWidget/util.d.ts +2 -37
  110. package/esm/BaseFeatureWidget/util.js +4 -85
  111. package/esm/CorePlugin.js +12 -7
  112. package/esm/PhasedScheduler.d.ts +4 -2
  113. package/esm/PhasedScheduler.js +18 -2
  114. package/esm/Plugin.d.ts +6 -1
  115. package/esm/Plugin.js +7 -0
  116. package/esm/PluginLoader.d.ts +55 -44
  117. package/esm/PluginLoader.js +290 -90
  118. package/esm/PluginManager.d.ts +476 -57
  119. package/esm/PluginManager.js +480 -91
  120. package/esm/ReExports/MuiDataGridReExports.d.ts +3 -2
  121. package/esm/ReExports/MuiDataGridReExports.js +58 -130
  122. package/esm/ReExports/MuiReExports.d.ts +3 -134
  123. package/esm/ReExports/MuiReExports.js +43 -16
  124. package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
  125. package/esm/ReExports/MuiStylesReExports.js +55 -0
  126. package/esm/ReExports/coreModules.generated.d.ts +2 -0
  127. package/esm/ReExports/coreModules.generated.js +528 -0
  128. package/esm/ReExports/coreWorkerModules.generated.d.ts +2 -0
  129. package/esm/ReExports/coreWorkerModules.generated.js +488 -0
  130. package/esm/ReExports/frameworkModules.d.ts +2 -0
  131. package/esm/ReExports/frameworkModules.js +68 -0
  132. package/esm/ReExports/frameworkShared.d.ts +12 -0
  133. package/esm/ReExports/frameworkShared.js +16 -0
  134. package/esm/ReExports/frameworkWorkerModules.generated.d.ts +2 -0
  135. package/esm/ReExports/frameworkWorkerModules.generated.js +130 -0
  136. package/esm/ReExports/lazify.d.ts +2 -2
  137. package/esm/ReExports/lazify.js +16 -3
  138. package/esm/ReExports/list.js +433 -160
  139. package/esm/ReExports/modules.d.ts +1 -1
  140. package/esm/ReExports/modules.js +10 -146
  141. package/esm/ReExports/muiComponentNames.d.ts +18 -0
  142. package/esm/ReExports/muiComponentNames.js +130 -0
  143. package/esm/ReExports/registry.d.ts +3 -0
  144. package/esm/ReExports/registry.js +46 -0
  145. package/esm/ReExports/uiStub.d.ts +3 -0
  146. package/esm/ReExports/uiStub.js +33 -0
  147. package/esm/ReExports/workerModules.d.ts +2 -0
  148. package/esm/ReExports/workerModules.js +11 -0
  149. package/esm/TextSearch/BaseResults.d.ts +20 -21
  150. package/esm/TextSearch/BaseResults.js +8 -33
  151. package/esm/TextSearch/TextSearchManager.d.ts +30 -36
  152. package/esm/TextSearch/TextSearchManager.js +138 -44
  153. package/esm/TextSearch/places.d.ts +12 -0
  154. package/esm/TextSearch/places.js +94 -0
  155. package/esm/assemblyManager/assembly.d.ts +310 -35
  156. package/esm/assemblyManager/assembly.js +554 -263
  157. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  158. package/esm/assemblyManager/assemblyAdapters.js +24 -0
  159. package/esm/assemblyManager/assemblyConfigSchema.d.ts +135 -19
  160. package/esm/assemblyManager/assemblyConfigSchema.js +205 -23
  161. package/esm/assemblyManager/assemblyManager.d.ts +586 -323
  162. package/esm/assemblyManager/assemblyManager.js +352 -51
  163. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +39 -0
  164. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +114 -0
  165. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  166. package/esm/assemblyManager/geneticCodes.js +44 -0
  167. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +19 -0
  168. package/esm/assemblyManager/getSequenceAdapterConfig.js +22 -0
  169. package/esm/assemblyManager/index.d.ts +1 -1
  170. package/esm/assemblyManager/index.js +2 -2
  171. package/esm/assemblyManager/indexAssemblyNames.d.ts +9 -0
  172. package/esm/assemblyManager/indexAssemblyNames.js +22 -0
  173. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  174. package/esm/assemblyManager/loadRefNameMap.js +75 -0
  175. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  176. package/esm/assemblyManager/refNameColors.js +32 -0
  177. package/esm/assemblyManager/refNameMapKey.d.ts +7 -0
  178. package/esm/assemblyManager/refNameMapKey.js +12 -0
  179. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  180. package/esm/assemblyManager/refNameMaps.js +87 -0
  181. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  182. package/esm/assemblyManager/refNameMismatch.js +66 -0
  183. package/esm/checkPlugins.d.ts +13 -0
  184. package/esm/checkPlugins.js +98 -0
  185. package/esm/configuration/bamIndexFields.d.ts +49 -0
  186. package/esm/configuration/bamIndexFields.js +41 -0
  187. package/esm/configuration/configurationSchema.d.ts +194 -29
  188. package/esm/configuration/configurationSchema.js +439 -145
  189. package/esm/configuration/configurationSchemaUnion.d.ts +39 -0
  190. package/esm/configuration/configurationSchemaUnion.js +56 -0
  191. package/esm/configuration/configurationSlot.d.ts +373 -30
  192. package/esm/configuration/configurationSlot.js +231 -224
  193. package/esm/configuration/fillLocations.d.ts +14 -0
  194. package/esm/configuration/fillLocations.js +14 -0
  195. package/esm/configuration/formatAboutConfigSchema.d.ts +41 -0
  196. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  197. package/esm/configuration/formatDetailsConfigSchema.d.ts +54 -0
  198. package/esm/configuration/formatDetailsConfigSchema.js +87 -0
  199. package/esm/configuration/fullConfSnapshot.d.ts +13 -0
  200. package/esm/configuration/fullConfSnapshot.js +44 -0
  201. package/esm/configuration/getConf.d.ts +92 -0
  202. package/esm/configuration/getConf.js +141 -0
  203. package/esm/configuration/index.d.ts +32 -3
  204. package/esm/configuration/index.js +27 -2
  205. package/esm/configuration/indexType.d.ts +26 -0
  206. package/esm/configuration/indexType.js +38 -0
  207. package/esm/configuration/mergeFormatCallbacks.d.ts +14 -0
  208. package/esm/configuration/mergeFormatCallbacks.js +27 -0
  209. package/esm/configuration/readConfObject.d.ts +34 -0
  210. package/esm/configuration/readConfObject.js +118 -0
  211. package/esm/configuration/requirements.d.ts +37 -0
  212. package/esm/configuration/requirements.js +88 -0
  213. package/esm/configuration/schemaRegistry.d.ts +52 -0
  214. package/esm/configuration/schemaRegistry.js +48 -0
  215. package/esm/configuration/schemaTypes.d.ts +39 -0
  216. package/esm/configuration/schemaTypes.js +105 -0
  217. package/esm/configuration/slotFacade.d.ts +65 -0
  218. package/esm/configuration/slotFacade.js +110 -0
  219. package/esm/configuration/slotValueUtils.d.ts +17 -0
  220. package/esm/configuration/slotValueUtils.js +25 -0
  221. package/esm/configuration/snapshotPreprocess.d.ts +43 -0
  222. package/esm/configuration/snapshotPreprocess.js +161 -0
  223. package/esm/configuration/tabixIndexFields.d.ts +70 -0
  224. package/esm/configuration/tabixIndexFields.js +62 -0
  225. package/esm/configuration/tabixShorthand.d.ts +51 -0
  226. package/esm/configuration/tabixShorthand.js +72 -0
  227. package/esm/configuration/types.d.ts +315 -13
  228. package/esm/configuration/uriShorthand.d.ts +9 -0
  229. package/esm/configuration/uriShorthand.js +16 -0
  230. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +19 -11
  231. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +19 -18
  232. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +158 -7
  233. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +164 -29
  234. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  235. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  236. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  237. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  238. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  239. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  240. package/esm/data_adapters/BaseAdapter/featureDensity.d.ts +40 -0
  241. package/esm/data_adapters/BaseAdapter/featureDensity.js +31 -0
  242. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  243. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  244. package/esm/data_adapters/BaseAdapter/index.d.ts +28 -6
  245. package/esm/data_adapters/BaseAdapter/index.js +6 -5
  246. package/esm/data_adapters/BaseAdapter/rowSources.d.ts +37 -0
  247. package/esm/data_adapters/BaseAdapter/rowSources.js +7 -0
  248. package/esm/data_adapters/BaseAdapter/stats.d.ts +37 -5
  249. package/esm/data_adapters/BaseAdapter/stats.js +89 -24
  250. package/esm/data_adapters/BaseAdapter/types.d.ts +11 -13
  251. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  252. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  253. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  254. package/esm/data_adapters/BaseAdapter/zoomRange.d.ts +10 -0
  255. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  256. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +5 -5
  257. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +34 -6
  258. package/esm/data_adapters/CytobandAdapter/configSchema.js +47 -17
  259. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  260. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  261. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  262. package/esm/data_adapters/dataAdapterCache.d.ts +53 -2
  263. package/esm/data_adapters/dataAdapterCache.js +99 -25
  264. package/esm/data_adapters/getFeatureAdapter.d.ts +24 -0
  265. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  266. package/esm/data_adapters/getSequenceSubAdapter.d.ts +19 -0
  267. package/esm/data_adapters/getSequenceSubAdapter.js +42 -0
  268. package/esm/pluggableElementTypes/AdapterType.d.ts +57 -7
  269. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  270. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  271. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  272. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  273. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  274. package/esm/pluggableElementTypes/DisplayType.d.ts +54 -14
  275. package/esm/pluggableElementTypes/DisplayType.js +30 -7
  276. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  277. package/esm/pluggableElementTypes/LazyStateModelElement.d.ts +32 -0
  278. package/esm/pluggableElementTypes/LazyStateModelElement.js +77 -0
  279. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +11 -0
  280. package/esm/pluggableElementTypes/PluggableElementBase.js +11 -0
  281. package/esm/pluggableElementTypes/RpcMethodType.d.ts +142 -12
  282. package/esm/pluggableElementTypes/RpcMethodType.js +279 -98
  283. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +18 -9
  284. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  285. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  286. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  287. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  288. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  289. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +7 -7
  290. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  291. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  292. package/esm/pluggableElementTypes/TrackType.js +1 -1
  293. package/esm/pluggableElementTypes/ViewType.d.ts +22 -5
  294. package/esm/pluggableElementTypes/ViewType.js +40 -5
  295. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  296. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  297. package/esm/pluggableElementTypes/addMenuItems.d.ts +88 -0
  298. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  299. package/esm/pluggableElementTypes/extendElementType.d.ts +29 -0
  300. package/esm/pluggableElementTypes/extendElementType.js +72 -0
  301. package/esm/pluggableElementTypes/index.d.ts +8 -7
  302. package/esm/pluggableElementTypes/index.js +24 -14
  303. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +80 -15
  304. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  305. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +643 -84
  306. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +230 -60
  307. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +246 -37
  308. package/esm/pluggableElementTypes/models/BaseTrackModel.js +416 -107
  309. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +236 -16
  310. package/esm/pluggableElementTypes/models/BaseViewModel.js +154 -16
  311. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +169 -25
  312. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  313. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +178 -0
  314. package/esm/pluggableElementTypes/models/assertDisplayContract.js +239 -0
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  1021. package/esm/util/revlist.js +14 -0
  1022. package/esm/util/rowStackGeometry.d.ts +66 -0
  1023. package/esm/util/rowStackGeometry.js +70 -0
  1024. package/esm/util/rpc.d.ts +16 -1
  1025. package/esm/util/rpc.js +12 -1
  1026. package/esm/util/rxjs.d.ts +30 -2
  1027. package/esm/util/rxjs.js +85 -10
  1028. package/esm/util/sameStrings.d.ts +16 -0
  1029. package/esm/util/sameStrings.js +20 -0
  1030. package/esm/util/samplesTsv.d.ts +49 -0
  1031. package/esm/util/samplesTsv.js +86 -0
  1032. package/esm/util/scheduleDetachedDestroy.d.ts +18 -0
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  1034. package/esm/util/scrollLatch.d.ts +5 -0
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  1036. package/esm/util/selectEncodedFeature.d.ts +16 -0
  1037. package/esm/util/selectEncodedFeature.js +34 -0
  1038. package/esm/util/selectNamedRegions.d.ts +136 -0
  1039. package/esm/util/selectNamedRegions.js +222 -0
  1040. package/esm/util/seqUtils.d.ts +17 -0
  1041. package/esm/util/seqUtils.js +80 -0
  1042. package/esm/util/sessionServices.d.ts +29 -0
  1043. package/esm/util/sessionServices.js +46 -0
  1044. package/esm/util/sessionSharing.d.ts +40 -0
  1045. package/esm/util/sessionSharing.js +154 -0
  1046. package/esm/util/sessionStorage.d.ts +1 -0
  1047. package/esm/util/sessionStorage.js +15 -0
  1048. package/esm/util/setStackTraceLimit.d.ts +6 -0
  1049. package/esm/util/setStackTraceLimit.js +20 -0
  1050. package/esm/util/shapeNameList.d.ts +2 -0
  1051. package/esm/util/shapeNameList.js +6 -0
  1052. package/esm/util/shapeNames.d.ts +7 -0
  1053. package/esm/util/shapeNames.js +11 -0
  1054. package/esm/util/simpleFeature.d.ts +111 -4
  1055. package/esm/util/simpleFeature.js +181 -29
  1056. package/esm/util/springAnimate.d.ts +20 -0
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  1060. package/esm/util/stats.d.ts +25 -2
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  1062. package/esm/util/stepTables.d.ts +82 -0
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  1064. package/esm/util/stringUtils.d.ts +5 -0
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  1074. package/esm/util/tags.d.ts +2 -0
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  1080. package/esm/util/tickLabels.d.ts +36 -0
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  1082. package/esm/util/timeGate.d.ts +25 -0
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  1084. package/esm/util/trackConfigDelta.d.ts +84 -0
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  1086. package/esm/util/tracks.d.ts +431 -30
  1087. package/esm/util/tracks.js +952 -185
  1088. package/esm/util/translateTranscript.d.ts +44 -0
  1089. package/esm/util/translateTranscript.js +102 -0
  1090. package/esm/util/tss-react/cssAndCx.js +11 -66
  1091. package/esm/util/tss-react/index.d.ts +11 -2
  1092. package/esm/util/tss-react/index.js +9 -2
  1093. package/esm/util/tss-react/makeStyles.js +7 -4
  1094. package/esm/util/tss-react/mergeClasses.js +1 -0
  1095. package/esm/util/tss-react/tools/classnames.d.ts +3 -0
  1096. package/esm/util/tss-react/tools/classnames.js +3 -0
  1097. package/esm/util/tss-react/tools/getDependencyArrayRef.d.ts +18 -0
  1098. package/esm/util/tss-react/tools/getDependencyArrayRef.js +19 -0
  1099. package/esm/util/tss-react/types.d.ts +1 -1
  1100. package/esm/util/tss-react/types.js +1 -6
  1101. package/esm/util/types/ElementId.js +1 -1
  1102. package/esm/util/types/data.d.ts +73 -0
  1103. package/esm/util/types/data.js +41 -0
  1104. package/esm/util/types/index.d.ts +459 -121
  1105. package/esm/util/types/index.js +96 -64
  1106. package/esm/util/types/isAny.d.ts +11 -0
  1107. package/esm/util/types/isAny.js +1 -0
  1108. package/esm/util/types/mst.d.ts +74 -47
  1109. package/esm/util/types/mst.js +31 -22
  1110. package/esm/util/types/predicate.d.ts +9 -0
  1111. package/esm/util/types/predicate.js +1 -0
  1112. package/esm/util/types/renameIds.d.ts +1 -0
  1113. package/esm/util/types/renameIds.js +29 -0
  1114. package/esm/util/types/renderingServices.d.ts +16 -0
  1115. package/esm/util/types/renderingServices.js +1 -0
  1116. package/esm/util/types/services.d.ts +55 -0
  1117. package/esm/util/types/services.js +10 -0
  1118. package/esm/util/types/util.d.ts +8 -2
  1119. package/esm/util/unknownSnapshotKeys.d.ts +51 -0
  1120. package/esm/util/unknownSnapshotKeys.js +82 -0
  1121. package/esm/util/unzip.d.ts +1 -0
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  1123. package/esm/util/useEventCallback.d.ts +1 -0
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  1125. package/esm/util/useFeatureSequence.d.ts +13 -7
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  1127. package/esm/util/useFetch.d.ts +55 -0
  1128. package/esm/util/useFetch.js +197 -0
  1129. package/esm/util/useFetchPlugins.d.ts +16 -0
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  1131. package/esm/util/useMeasure.d.ts +11 -1
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  1133. package/esm/util/usePanZoom.d.ts +75 -0
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  1135. package/esm/util/usePanelVirtualScroll.d.ts +9 -0
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  1137. package/esm/util/usePointerDrag.d.ts +37 -0
  1138. package/esm/util/usePointerDrag.js +61 -0
  1139. package/esm/util/useRafCommit.d.ts +4 -0
  1140. package/esm/util/useRafCommit.js +50 -0
  1141. package/esm/util/useResizeDrag.d.ts +91 -0
  1142. package/esm/util/useResizeDrag.js +105 -0
  1143. package/esm/util/useRowVirtualScroll.d.ts +9 -0
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  1145. package/esm/util/useVirtualScrollWheel.d.ts +23 -0
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  1147. package/esm/util/viewHighlights.d.ts +3 -0
  1148. package/esm/util/viewHighlights.js +5 -0
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  1151. package/esm/util/virtualRange.d.ts +36 -0
  1152. package/esm/util/virtualRange.js +26 -0
  1153. package/esm/util/webStorage.d.ts +26 -0
  1154. package/esm/util/webStorage.js +92 -0
  1155. package/esm/util/wheelZoom.d.ts +65 -0
  1156. package/esm/util/wheelZoom.js +297 -0
  1157. package/esm/util/whenViewSettled.d.ts +74 -0
  1158. package/esm/util/whenViewSettled.js +77 -0
  1159. package/esm/util/withFeatureDetails.d.ts +34 -0
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  1161. package/esm/util/withLaunchInput.d.ts +174 -0
  1162. package/esm/util/withLaunchInput.js +274 -0
  1163. package/package.json +290 -820
  1164. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +0 -2
  1165. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +0 -14
  1166. package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +0 -7
  1167. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +0 -80
  1168. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.js +0 -583
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  1171. package/esm/ReExports/BaseFeatureDetails.d.ts +0 -1
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  1177. package/esm/configuration/util.d.ts +0 -10
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  1179. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
  1180. package/esm/data_adapters/util.d.ts +0 -1
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  1263. /package/esm/{BaseFeatureWidget/BaseFeatureDetail/types.js → data_adapters/BaseAdapter/CytobandAdapter.js} +0 -0
  1264. /package/esm/data_adapters/BaseAdapter/{BaseOptions.js → zoomRange.js} +0 -0
  1265. /package/esm/{util/layouts/BaseLayout.js → rpc/RpcRegistry.js} +0 -0
@@ -0,0 +1,189 @@
1
+ import { makeAbortError } from '../util/aborting.js';
2
+ import { deserializeError } from './serializeError/index.js';
3
+ export default class RpcClient {
4
+ worker;
5
+ pending = new Map();
6
+ destroyed = false;
7
+ events = new Map();
8
+ counter = 0;
9
+ constructor(worker) {
10
+ this.worker = worker;
11
+ this.worker.addEventListener('message', e => {
12
+ this.handler(e);
13
+ });
14
+ this.worker.addEventListener('error', e => {
15
+ this.catch(e);
16
+ });
17
+ // A frame this realm could not DESERIALIZE, as opposed to `error`, which is
18
+ // the worker's script throwing. It carries no uid, so the reply it lost
19
+ // cannot be identified and settling everything is the only move — the same
20
+ // one `catch` makes, and better than a display spinning on a promise that
21
+ // can never settle. The worker itself is left alone: it is still healthy,
22
+ // and a plugin's own non-libRpc traffic on it can be what failed.
23
+ this.worker.addEventListener('messageerror', () => {
24
+ this.rejectAllPending(new Error('an RPC worker message could not be deserialized'));
25
+ });
26
+ }
27
+ on(event, listener) {
28
+ const listeners = this.events.get(event);
29
+ if (listeners) {
30
+ listeners.push(listener);
31
+ }
32
+ else {
33
+ this.events.set(event, [listener]);
34
+ }
35
+ return this;
36
+ }
37
+ off(event, listener) {
38
+ const listeners = this.events.get(event);
39
+ if (listeners) {
40
+ const idx = listeners.indexOf(listener);
41
+ if (idx !== -1) {
42
+ listeners.splice(idx, 1);
43
+ }
44
+ // drop the emptied key, not just the listener: every reporting call
45
+ // mints its own status channel (WebWorkerHandle.call), so a retained
46
+ // empty array is one dead Map entry per call for the life of the page
47
+ if (listeners.length === 0) {
48
+ this.events.delete(event);
49
+ }
50
+ }
51
+ return this;
52
+ }
53
+ emit(event, data) {
54
+ const listeners = this.events.get(event);
55
+ if (listeners) {
56
+ // over a copy: a listener that removes itself splices the live array, and
57
+ // a `for...of` over that skips whichever listener moved down into the
58
+ // index it just read
59
+ for (const listener of [...listeners]) {
60
+ listener(data);
61
+ }
62
+ }
63
+ return this;
64
+ }
65
+ handler(e) {
66
+ const { uid, error, eventName, data, libRpc } = e.data;
67
+ if (!libRpc) {
68
+ return;
69
+ }
70
+ // three frame kinds share the channel: an error (rejects the call), a
71
+ // named event (status side-channel), and — the default — a call reply.
72
+ //
73
+ // Which KIND the frame is, never whether its payload looks useful. A truthy
74
+ // test read `error: ''` as a reply and resolved the call with `undefined`,
75
+ // and an empty message is exactly what `RpcServer.throw`'s last-resort
76
+ // fallback can produce — so the guard against an unsettleable call turned
77
+ // one class of failure into a wrong value instead. `resolve(uid, undefined)`
78
+ // then reaches `deserializeReturn` and the caller reads fields off nothing,
79
+ // blaming its own display.
80
+ if (error !== undefined) {
81
+ this.reject(uid, error);
82
+ }
83
+ else if (eventName) {
84
+ this.emit(eventName, data);
85
+ }
86
+ else {
87
+ this.resolve(uid, data);
88
+ }
89
+ }
90
+ // terminating a worker settles nothing on its own: a pending call's reply can
91
+ // never arrive, so reject it here instead of leaving the caller's promise (and
92
+ // everything its continuation holds) unsettled forever
93
+ destroy() {
94
+ this.destroyed = true;
95
+ this.rejectAllPending(new Error('RPC worker was terminated'));
96
+ this.events.clear();
97
+ }
98
+ rejectAllPending(error) {
99
+ // snapshot before clearing so a synchronous reject handler that schedules
100
+ // a new call() can't have its entry dropped by the clear()
101
+ const snapshot = [...this.pending.values()];
102
+ this.pending.clear();
103
+ for (const { reject } of snapshot) {
104
+ reject(error);
105
+ }
106
+ }
107
+ catch(e) {
108
+ this.rejectAllPending(new Error(e.message));
109
+ this.emit('error', {
110
+ message: e.message,
111
+ lineno: e.lineno,
112
+ filename: e.filename,
113
+ });
114
+ }
115
+ reject(uid, error) {
116
+ const p = this.pending.get(uid);
117
+ if (p) {
118
+ p.reject(deserializeError(error));
119
+ this.pending.delete(uid);
120
+ }
121
+ }
122
+ resolve(uid, data) {
123
+ const p = this.pending.get(uid);
124
+ if (p) {
125
+ p.resolve(data);
126
+ this.pending.delete(uid);
127
+ }
128
+ }
129
+ /**
130
+ * Abort the call `uid`, so the signal it runs under in the worker aborts.
131
+ * Fire-and-forget: it settles no pending call, and a worker no longer running
132
+ * that call ignores it.
133
+ */
134
+ abort(uid) {
135
+ this.worker.postMessage({ abort: uid, libRpc: true });
136
+ }
137
+ /**
138
+ * No transfer list: transferables flow only worker → main, in a reply's
139
+ * rpcResult wrapper. Transferring an argument would neuter the main thread's
140
+ * own buffer — this took an option for one and nothing ever passed it.
141
+ *
142
+ * With a `signal`, the worker runs the method under a signal of its own and
143
+ * aborts it when this one aborts. The uid is the call's identity on both
144
+ * sides, so the abort frame needs nothing else; the listener is attached
145
+ * before the call frame is posted and removed when the call settles, so an
146
+ * abort in between reaches a worker still running the call, and one after
147
+ * reaches nothing.
148
+ */
149
+ call(method, data, signal) {
150
+ const uid = String(++this.counter);
151
+ return new Promise((resolve, reject) => {
152
+ if (this.destroyed) {
153
+ reject(new Error('RPC worker was terminated'));
154
+ return;
155
+ }
156
+ if (signal?.aborted) {
157
+ reject(makeAbortError());
158
+ return;
159
+ }
160
+ const onAbort = () => {
161
+ this.abort(uid);
162
+ };
163
+ signal?.addEventListener('abort', onAbort, { once: true });
164
+ const detach = () => {
165
+ signal?.removeEventListener('abort', onAbort);
166
+ };
167
+ this.pending.set(uid, {
168
+ resolve: value => {
169
+ detach();
170
+ resolve(value);
171
+ },
172
+ reject: error => {
173
+ detach();
174
+ reject(error);
175
+ },
176
+ });
177
+ try {
178
+ this.worker.postMessage({ method, uid, data, libRpc: true, abortable: signal !== undefined }, []);
179
+ }
180
+ catch (e) {
181
+ // a non-cloneable payload throws here, which rejects this promise; drop
182
+ // the entry that is now waiting on a reply the worker never received
183
+ this.pending.delete(uid);
184
+ detach();
185
+ throw e;
186
+ }
187
+ });
188
+ }
189
+ }
@@ -1,35 +1,128 @@
1
- import MainThreadRpcDriver from './MainThreadRpcDriver.ts';
2
- import WebWorkerRpcDriver from './WebWorkerRpcDriver.ts';
3
- import type BaseRpcDriver from './BaseRpcDriver.ts';
4
1
  import type PluginManager from '../PluginManager.ts';
5
2
  import type { AnyConfigurationModel } from '../configuration/index.ts';
6
- type DriverClass = BaseRpcDriver;
7
- interface BackendConfigurations {
8
- WebWorkerRpcDriver?: Omit<ConstructorParameters<typeof WebWorkerRpcDriver>[0], 'config'>;
9
- MainThreadRpcDriver?: Omit<ConstructorParameters<typeof MainThreadRpcDriver>[0], 'config'>;
10
- [key: string]: unknown;
3
+ import type BaseRpcDriver from './BaseRpcDriver.ts';
4
+ import type { RpcCallArgs, RpcCallReturn } from './RpcRegistry.ts';
5
+ export interface RpcManagerOptions {
6
+ makeWorkerInstance?: () => Worker;
7
+ defaultDriverName?: string;
11
8
  }
12
- export type RpcDriverFactory = (config: AnyConfigurationModel, backendConfig: unknown, pluginManager: PluginManager) => BaseRpcDriver;
13
9
  export default class RpcManager {
14
- pluginManager: PluginManager;
15
- mainConfiguration: AnyConfigurationModel;
16
- backendConfigurations: BackendConfigurations;
17
10
  static configSchema: import("../configuration/configurationSchema.ts").ConfigurationSchemaType<{
18
- defaultDriver: {
19
- type: string;
20
- description: string;
11
+ readonly defaultDriver: {
12
+ type: "string";
13
+ } & {
21
14
  defaultValue: string;
22
15
  };
23
- drivers: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> | undefined, import("@jbrowse/mobx-state-tree").ModelSnapshotType<Record<string, any>>, ({} & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject) | undefined>>, [undefined]>;
24
- }, import("../configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
25
- driverObjects: Map<string, DriverClass>;
26
- driverFactories: Map<string, RpcDriverFactory>;
27
- constructor(pluginManager: PluginManager, mainConfiguration: AnyConfigurationModel, backendConfigurations: BackendConfigurations);
28
- registerDriverFactory(name: string, factory: RpcDriverFactory): void;
29
- getDriver(backendName: string): BaseRpcDriver;
30
- getDriverForCall(_sessionId: string, _functionName: string, args: {
31
- rpcDriverName?: string;
32
- }): Promise<BaseRpcDriver>;
33
- call(sessionId: string, functionName: string, args: Record<string, unknown>, opts?: {}): Promise<unknown>;
16
+ readonly workerCount: {
17
+ type: "number";
18
+ } & {
19
+ defaultValue: number;
20
+ };
21
+ }, import("../configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined, undefined, import("../configuration/requirements.ts").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
22
+ private pluginManager;
23
+ private mainConfiguration;
24
+ private hostDriverName;
25
+ private makeWorkerInstance?;
26
+ private driver?;
27
+ private destroyed;
28
+ constructor(pluginManager: PluginManager, mainConfiguration: AnyConfigurationModel, { makeWorkerInstance, defaultDriverName, }?: RpcManagerOptions);
29
+ /**
30
+ * Which driver this session runs on: the config's `defaultDriver` if set,
31
+ * otherwise the host application's default.
32
+ *
33
+ * A getter rather than the two fields it replaces, because the diagnostic
34
+ * surfaces that want to print it — the About widget and the error-stack dialog
35
+ * — were each re-deriving the resolution from `mainConfiguration` and
36
+ * `defaultDriverName`, so the rule for where a call goes was written three
37
+ * times and one copy carried a cast.
38
+ */
39
+ get driverName(): string;
40
+ /**
41
+ * The driver itself, built once and kept. The config read above is a tracked
42
+ * MobX read and `call` reaches it synchronously, so resolving per call also
43
+ * made the RPC configuration a dependency of every autorun that fetches.
44
+ *
45
+ * There is no per-call, per-track or per-display override. One existed, and
46
+ * one call site in the app ever passed it — a tag-value scan in the alignments
47
+ * plugin — so a track pinned to the main thread had its tag scan run there and
48
+ * every one of its data fetches go to the worker pool anyway. Routing a single
49
+ * call somewhere else is only meaningful with a backend that differs in what it
50
+ * can do, which is the tabled server-side-driver idea; add it back with that,
51
+ * not before.
52
+ *
53
+ * There is no registry of driver factories either: naming a driver means
54
+ * naming `BaseRpcDriver`, which `@jbrowse/core` has no export path for, so
55
+ * the two built-ins below are the whole set. ADR-086.
56
+ */
57
+ getDriver(): BaseRpcDriver;
58
+ private makeDriver;
59
+ /**
60
+ * `args` carries the method's data and the caller's handles on the operation —
61
+ * the signal and the status callback. Both handles are always accepted,
62
+ * for every method, because {@link RpcHandles} is part of `RpcCallArgs` rather
63
+ * than of any registry entry.
64
+ *
65
+ * There is deliberately no second position for either. The handles were
66
+ * accepted in an `opts` parameter as well, and the two disagreed:
67
+ * `WebWorkerRpcDriver` honored a `statusCallback` there and
68
+ * `MainThreadRpcDriver` ignored `opts` entirely, so the same call had a
69
+ * working progress bar under a worker and a silent one under the driver every
70
+ * embedded component defaults to. One position.
71
+ *
72
+ * The cast on the way out is at the driver boundary, where the method is an
73
+ * unparameterized {@link RpcMethodType} and `deserializeReturn` is therefore
74
+ * `unknown`. It is not the only thing holding the return type up: the same
75
+ * type is what that hook is declared to produce, checked against the registry
76
+ * at each method that overrides it.
77
+ */
78
+ call<M extends string>(sessionId: string, functionName: M, args: RpcCallArgs<M>): Promise<RpcCallReturn<M>>;
79
+ /**
80
+ * Drop everything held for a session — the worker-side adapter cache, and the
81
+ * driver's own bookkeeping for it. Reached from `releaseAdapterSession` when
82
+ * the last track model holding an `rpcSessionId` goes away.
83
+ *
84
+ * A lifecycle operation rather than `call(sessionId, 'CoreFreeResources')`,
85
+ * so that it neither boots a transport to free a session that never used one
86
+ * nor outlives {@link destroy}; see {@link BaseRpcDriver.freeSession}.
87
+ *
88
+ * Silent on a destroyed manager, because the destroy already freed strictly
89
+ * more than this would: it terminated the workers the cache lived in.
90
+ */
91
+ freeSession(sessionId: string): Promise<void>;
92
+ /**
93
+ * Run an RPC thunk, and if it fails because a location needs auth, set up
94
+ * credentials for the origin and run it exactly once more. The single retry
95
+ * is structural — there is no loop — so a persistent auth failure surfaces
96
+ * the error instead of spinning. The retry re-runs serializeArguments, which
97
+ * now finds the new account and injects pre-authorization (prompting the
98
+ * user). If auth can't be set up, the original error is rethrown unchanged.
99
+ */
100
+ private withAuthRetry;
101
+ /**
102
+ * Ensure an ephemeral HTTP-basic internet account exists for a location's
103
+ * origin so a retried RPC call can authenticate. The account id is derived
104
+ * from the origin and reused if already present: when a track first loads,
105
+ * many block RPC calls fail auth near-simultaneously, and a single shared
106
+ * account collapses them into one credential prompt (BaseInternetAccountModel
107
+ * memoizes the token via a per-account promise). Returns false when the root
108
+ * model can't hold accounts or no HTTPBasicInternetAccount type is registered
109
+ * (authentication plugin not loaded), signaling the caller not to retry.
110
+ */
111
+ private ensureAuthForOrigin;
112
+ /**
113
+ * Terminate the driver's worker threads. Call when discarding the owning root
114
+ * model (e.g. switching sessions or reloading after a plugin change) so
115
+ * orphaned workers don't accumulate across a desktop run.
116
+ *
117
+ * **Terminal.** ADR-069 destroys the tree a task after `detach()`, so calls
118
+ * still arrive in that gap; a later one throws rather than quietly building a
119
+ * second driver and a second pool that nothing will ever destroy. ADR-086.
120
+ */
121
+ destroy(): void;
122
+ /**
123
+ * Build the driver and let it start what the first call would wait for — a
124
+ * web worker's bundle and runtime plugins — while the host is still building
125
+ * its session.
126
+ */
127
+ warmUp(): void;
34
128
  }
35
- export {};
@@ -1,63 +1,200 @@
1
- import MainThreadRpcDriver from "./MainThreadRpcDriver.js";
2
- import WebWorkerRpcDriver from "./WebWorkerRpcDriver.js";
3
- import rpcConfigSchema from "./configSchema.js";
4
- import { readConfObject } from "../configuration/index.js";
1
+ import { readConfObject } from '../configuration/index.js';
2
+ import { getNumberGrouping } from '../util/numericUtils.js';
3
+ import { isAppRootModel, isAuthNeededException } from '../util/types/index.js';
4
+ import MainThreadRpcDriver from './MainThreadRpcDriver.js';
5
+ import WebWorkerRpcDriver from './WebWorkerRpcDriver.js';
6
+ import rpcConfigSchema from './configSchema.js';
5
7
  export default class RpcManager {
8
+ static configSchema = rpcConfigSchema;
6
9
  pluginManager;
7
10
  mainConfiguration;
8
- backendConfigurations;
9
- static configSchema = rpcConfigSchema;
10
- driverObjects;
11
- driverFactories;
12
- constructor(pluginManager, mainConfiguration, backendConfigurations) {
11
+ hostDriverName;
12
+ makeWorkerInstance;
13
+ driver;
14
+ destroyed = false;
15
+ constructor(pluginManager, mainConfiguration, { makeWorkerInstance, defaultDriverName = 'MainThreadRpcDriver', } = {}) {
13
16
  this.pluginManager = pluginManager;
14
17
  this.mainConfiguration = mainConfiguration;
15
- this.backendConfigurations = backendConfigurations;
16
- this.driverObjects = new Map();
17
- this.driverFactories = new Map();
18
- this.registerDriverFactory('MainThreadRpcDriver', (config, backendConfig) => new MainThreadRpcDriver({
19
- ...backendConfig,
20
- config,
21
- }));
22
- this.registerDriverFactory('WebWorkerRpcDriver', (config, backendConfig, pm) => new WebWorkerRpcDriver({
23
- ...backendConfig,
24
- config,
25
- }, {
26
- plugins: pm.runtimePluginDefinitions,
27
- windowHref: typeof window !== 'undefined' ? window.location.href : '',
28
- }));
29
- }
30
- registerDriverFactory(name, factory) {
31
- this.driverFactories.set(name, factory);
32
- }
33
- getDriver(backendName) {
34
- const existingDriver = this.driverObjects.get(backendName);
35
- if (existingDriver) {
36
- return existingDriver;
37
- }
38
- const factory = this.driverFactories.get(backendName);
39
- if (!factory) {
40
- throw new Error(`RPC driver "${backendName}" is not registered`);
41
- }
42
- const backendConfig = this.backendConfigurations[backendName];
43
- if (!backendConfig) {
44
- throw new Error(`RPC driver "${backendName}" is missing configuration`);
18
+ this.hostDriverName = defaultDriverName;
19
+ this.makeWorkerInstance = makeWorkerInstance;
20
+ }
21
+ /**
22
+ * Which driver this session runs on: the config's `defaultDriver` if set,
23
+ * otherwise the host application's default.
24
+ *
25
+ * A getter rather than the two fields it replaces, because the diagnostic
26
+ * surfaces that want to print it — the About widget and the error-stack dialog
27
+ * — were each re-deriving the resolution from `mainConfiguration` and
28
+ * `defaultDriverName`, so the rule for where a call goes was written three
29
+ * times and one copy carried a cast.
30
+ */
31
+ get driverName() {
32
+ return (readConfObject(this.mainConfiguration, 'defaultDriver') ||
33
+ this.hostDriverName);
34
+ }
35
+ /**
36
+ * The driver itself, built once and kept. The config read above is a tracked
37
+ * MobX read and `call` reaches it synchronously, so resolving per call also
38
+ * made the RPC configuration a dependency of every autorun that fetches.
39
+ *
40
+ * There is no per-call, per-track or per-display override. One existed, and
41
+ * one call site in the app ever passed it — a tag-value scan in the alignments
42
+ * plugin — so a track pinned to the main thread had its tag scan run there and
43
+ * every one of its data fetches go to the worker pool anyway. Routing a single
44
+ * call somewhere else is only meaningful with a backend that differs in what it
45
+ * can do, which is the tabled server-side-driver idea; add it back with that,
46
+ * not before.
47
+ *
48
+ * There is no registry of driver factories either: naming a driver means
49
+ * naming `BaseRpcDriver`, which `@jbrowse/core` has no export path for, so
50
+ * the two built-ins below are the whole set. ADR-086.
51
+ */
52
+ getDriver() {
53
+ if (this.destroyed) {
54
+ throw new Error('RpcManager was destroyed');
45
55
  }
46
- const config = this.mainConfiguration.drivers.get('WebWorkerRpcDriver');
47
- const newDriver = factory(config, backendConfig, this.pluginManager);
48
- this.driverObjects.set(backendName, newDriver);
49
- return newDriver;
56
+ return (this.driver ??= this.makeDriver(this.driverName));
50
57
  }
51
- async getDriverForCall(_sessionId, _functionName, args) {
52
- const backendName = args.rpcDriverName ||
53
- readConfObject(this.mainConfiguration, 'defaultDriver');
54
- return this.getDriver(backendName);
58
+ makeDriver(backendName) {
59
+ if (backendName === 'MainThreadRpcDriver') {
60
+ return new MainThreadRpcDriver(this.pluginManager, this.mainConfiguration);
61
+ }
62
+ else if (backendName === 'WebWorkerRpcDriver') {
63
+ const { makeWorkerInstance } = this;
64
+ if (!makeWorkerInstance) {
65
+ throw new Error('WebWorkerRpcDriver requested but no makeWorkerInstance was provided');
66
+ }
67
+ return new WebWorkerRpcDriver(this.pluginManager, this.mainConfiguration, {
68
+ makeWorkerInstance,
69
+ plugins: this.pluginManager.runtimePluginDefinitions,
70
+ windowHref: typeof window === 'undefined' ? '' : window.location.href,
71
+ // workers format their own strings (a jexl `mouseover` slot runs
72
+ // against the full feature worker-side), so they need the display
73
+ // preference too. Read at driver construction — workers boot lazily and
74
+ // are not rebooted on a preference change, which is why the preference
75
+ // asks for a reload.
76
+ numberGrouping: getNumberGrouping(),
77
+ });
78
+ }
79
+ else {
80
+ throw new Error(`RPC driver "${backendName}" is not registered`);
81
+ }
55
82
  }
56
- async call(sessionId, functionName, args, opts = {}) {
83
+ /**
84
+ * `args` carries the method's data and the caller's handles on the operation —
85
+ * the signal and the status callback. Both handles are always accepted,
86
+ * for every method, because {@link RpcHandles} is part of `RpcCallArgs` rather
87
+ * than of any registry entry.
88
+ *
89
+ * There is deliberately no second position for either. The handles were
90
+ * accepted in an `opts` parameter as well, and the two disagreed:
91
+ * `WebWorkerRpcDriver` honored a `statusCallback` there and
92
+ * `MainThreadRpcDriver` ignored `opts` entirely, so the same call had a
93
+ * working progress bar under a worker and a silent one under the driver every
94
+ * embedded component defaults to. One position.
95
+ *
96
+ * The cast on the way out is at the driver boundary, where the method is an
97
+ * unparameterized {@link RpcMethodType} and `deserializeReturn` is therefore
98
+ * `unknown`. It is not the only thing holding the return type up: the same
99
+ * type is what that hook is declared to produce, checked against the registry
100
+ * at each method that overrides it.
101
+ */
102
+ async call(sessionId, functionName, args) {
57
103
  if (!sessionId) {
58
104
  throw new Error('sessionId is required');
59
105
  }
60
- const driverForCall = await this.getDriverForCall(sessionId, functionName, args);
61
- return driverForCall.call(this.pluginManager, sessionId, functionName, args, opts);
106
+ const driverForCall = this.getDriver();
107
+ return (await this.withAuthRetry(() => driverForCall.call(sessionId, functionName, { ...args, sessionId })));
108
+ }
109
+ /**
110
+ * Drop everything held for a session — the worker-side adapter cache, and the
111
+ * driver's own bookkeeping for it. Reached from `releaseAdapterSession` when
112
+ * the last track model holding an `rpcSessionId` goes away.
113
+ *
114
+ * A lifecycle operation rather than `call(sessionId, 'CoreFreeResources')`,
115
+ * so that it neither boots a transport to free a session that never used one
116
+ * nor outlives {@link destroy}; see {@link BaseRpcDriver.freeSession}.
117
+ *
118
+ * Silent on a destroyed manager, because the destroy already freed strictly
119
+ * more than this would: it terminated the workers the cache lived in.
120
+ */
121
+ async freeSession(sessionId) {
122
+ if (!this.destroyed) {
123
+ await this.getDriver().freeSession(sessionId);
124
+ }
125
+ }
126
+ /**
127
+ * Run an RPC thunk, and if it fails because a location needs auth, set up
128
+ * credentials for the origin and run it exactly once more. The single retry
129
+ * is structural — there is no loop — so a persistent auth failure surfaces
130
+ * the error instead of spinning. The retry re-runs serializeArguments, which
131
+ * now finds the new account and injects pre-authorization (prompting the
132
+ * user). If auth can't be set up, the original error is rethrown unchanged.
133
+ */
134
+ async withAuthRetry(run) {
135
+ try {
136
+ return await run();
137
+ }
138
+ catch (error) {
139
+ if (isAuthNeededException(error) && this.ensureAuthForOrigin(error.url)) {
140
+ return run();
141
+ }
142
+ else {
143
+ throw error;
144
+ }
145
+ }
146
+ }
147
+ /**
148
+ * Ensure an ephemeral HTTP-basic internet account exists for a location's
149
+ * origin so a retried RPC call can authenticate. The account id is derived
150
+ * from the origin and reused if already present: when a track first loads,
151
+ * many block RPC calls fail auth near-simultaneously, and a single shared
152
+ * account collapses them into one credential prompt (BaseInternetAccountModel
153
+ * memoizes the token via a per-account promise). Returns false when the root
154
+ * model can't hold accounts or no HTTPBasicInternetAccount type is registered
155
+ * (authentication plugin not loaded), signaling the caller not to retry.
156
+ */
157
+ ensureAuthForOrigin(url) {
158
+ const { rootModel } = this.pluginManager;
159
+ let ready = false;
160
+ if (isAppRootModel(rootModel)) {
161
+ try {
162
+ const internetAccountId = `HTTPBasicInternetAccount-${new URL(url).origin}`;
163
+ const hasExisting = rootModel.internetAccounts.some(account => account.internetAccountId === internetAccountId);
164
+ if (!hasExisting) {
165
+ rootModel.createEphemeralInternetAccount(internetAccountId, {}, url);
166
+ }
167
+ ready = true;
168
+ }
169
+ catch {
170
+ // no HTTPBasicInternetAccount type registered; leave ready=false so the
171
+ // caller surfaces the original auth error instead of retrying
172
+ }
173
+ }
174
+ return ready;
175
+ }
176
+ /**
177
+ * Terminate the driver's worker threads. Call when discarding the owning root
178
+ * model (e.g. switching sessions or reloading after a plugin change) so
179
+ * orphaned workers don't accumulate across a desktop run.
180
+ *
181
+ * **Terminal.** ADR-069 destroys the tree a task after `detach()`, so calls
182
+ * still arrive in that gap; a later one throws rather than quietly building a
183
+ * second driver and a second pool that nothing will ever destroy. ADR-086.
184
+ */
185
+ destroy() {
186
+ this.destroyed = true;
187
+ this.driver?.destroy();
188
+ this.driver = undefined;
189
+ }
190
+ /**
191
+ * Build the driver and let it start what the first call would wait for — a
192
+ * web worker's bundle and runtime plugins — while the host is still building
193
+ * its session.
194
+ */
195
+ warmUp() {
196
+ if (!this.destroyed) {
197
+ this.getDriver().warmUp();
198
+ }
62
199
  }
63
200
  }