@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
  1033. package/esm/util/scheduleDetachedDestroy.js +24 -0
  1034. package/esm/util/scrollLatch.d.ts +5 -0
  1035. package/esm/util/scrollLatch.js +67 -0
  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
  1057. package/esm/util/springAnimate.js +80 -0
  1058. package/esm/util/starFusion.d.ts +26 -0
  1059. package/esm/util/starFusion.js +37 -0
  1060. package/esm/util/stats.d.ts +25 -2
  1061. package/esm/util/stats.js +39 -8
  1062. package/esm/util/stepTables.d.ts +82 -0
  1063. package/esm/util/stepTables.js +243 -0
  1064. package/esm/util/stringUtils.d.ts +5 -0
  1065. package/esm/util/stringUtils.js +34 -0
  1066. package/esm/util/svAlt.d.ts +145 -0
  1067. package/esm/util/svAlt.js +364 -0
  1068. package/esm/util/svgColorProps.d.ts +18 -0
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  1070. package/esm/util/systemColorScheme.d.ts +12 -0
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  1072. package/esm/util/tabix.d.ts +125 -0
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  1074. package/esm/util/tags.d.ts +2 -0
  1075. package/esm/util/tags.js +5 -0
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  1078. package/esm/util/thresholdScale.d.ts +91 -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
  1085. package/esm/util/trackConfigDelta.js +206 -0
  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
  1122. package/esm/util/unzip.js +6 -0
  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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  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
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  1143. package/esm/util/useRowVirtualScroll.d.ts +9 -0
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  1145. package/esm/util/useVirtualScrollWheel.d.ts +23 -0
  1146. package/esm/util/useVirtualScrollWheel.js +74 -0
  1147. package/esm/util/viewHighlights.d.ts +3 -0
  1148. package/esm/util/viewHighlights.js +5 -0
  1149. package/esm/util/viewStatus.d.ts +90 -0
  1150. package/esm/util/viewStatus.js +54 -0
  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
  1160. package/esm/util/withFeatureDetails.js +59 -0
  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
  1169. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +0 -141
  1170. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.js +0 -1116
  1171. package/esm/ReExports/BaseFeatureDetails.d.ts +0 -1
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  1173. package/esm/ReExports/DataGrid.d.ts +0 -1
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  1175. package/esm/ReExports/index.d.ts +0 -1
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  1177. package/esm/configuration/util.d.ts +0 -10
  1178. package/esm/configuration/util.js +0 -123
  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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  1182. package/esm/pluggableElementTypes/GlyphType.d.ts +0 -43
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  1194. package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
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  1257. package/esm/util/tss-react/mui/index.d.ts +0 -1
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  1264. /package/esm/data_adapters/BaseAdapter/{BaseOptions.js → zoomRange.js} +0 -0
  1265. /package/esm/{util/layouts/BaseLayout.js → rpc/RpcRegistry.js} +0 -0
@@ -1,31 +1,85 @@
1
1
  import BaseRpcDriver from './BaseRpcDriver.ts';
2
- import type { RpcDriverConstructorArgs } from './BaseRpcDriver.ts';
3
- import type { PluginDefinition } from '../PluginLoader.ts';
4
- interface WebWorkerRpcDriverConstructorArgs extends RpcDriverConstructorArgs {
5
- makeWorkerInstance: () => Worker;
2
+ import type PluginManager from '../PluginManager.ts';
3
+ import type { AnyConfigurationModel } from '../configuration/index.ts';
4
+ import type RpcMethodType from '../pluggableElementTypes/RpcMethodType.ts';
5
+ import type { PluginDefinition } from '../pluginDefinitions.ts';
6
+ import type { StatusCallback } from '../util/progress.ts';
7
+ import type { RpcHandles } from './RpcRegistry.ts';
8
+ export interface WorkerHandle {
9
+ destroy(): void;
10
+ onError?(callback: () => void): void;
11
+ on?(eventName: string, listener: (data: unknown) => void): void;
12
+ postMessage?(message: unknown): void;
13
+ call(functionName: string, args?: unknown, options?: {
14
+ statusCallback?: StatusCallback;
15
+ signal?: AbortSignal;
16
+ }): Promise<unknown>;
6
17
  }
7
- interface Options {
8
- statusCallback?: (arg0: unknown) => void;
9
- rpcDriverClassName: string;
18
+ declare module '@jbrowse/core/PluginManager' {
19
+ interface ExtensionPointRegistry {
20
+ 'Core-extendWorker': {
21
+ args: WorkerHandle;
22
+ result: WorkerHandle;
23
+ };
24
+ }
10
25
  }
11
- declare class WebWorkerHandle {
12
- worker: Worker;
13
- private client;
14
- constructor(worker: Worker);
15
- destroy(): void;
16
- call(funcName: string, args: Record<string, unknown>, opts: Options): Promise<unknown>;
26
+ export interface WebWorkerRpcDriverOptions {
27
+ makeWorkerInstance: () => Worker;
28
+ plugins: PluginDefinition[];
29
+ windowHref: string;
30
+ numberGrouping: boolean;
17
31
  }
32
+ /**
33
+ * Runs RPC methods in a pool of lazily-booted web workers, with our own
34
+ * state-group-aware round-robin assignment (one sticky worker per session) so a
35
+ * session's calls land on the same worker and can share cached adapters.
36
+ *
37
+ * The pool is here rather than in a `WorkerPoolRpcDriver` above it: that base
38
+ * abstracted `makeWorker`, which has one implementation. It is a plain
39
+ * overridable method now, which is all the seam was ever used for. ADR-086.
40
+ */
18
41
  export default class WebWorkerRpcDriver extends BaseRpcDriver {
19
- workerBootConfiguration: {
20
- plugins: PluginDefinition[];
21
- windowHref: string;
22
- };
42
+ private options;
23
43
  name: string;
24
- makeWorkerInstance: () => Worker;
25
- constructor(args: WebWorkerRpcDriverConstructorArgs, workerBootConfiguration: {
26
- plugins: PluginDefinition[];
27
- windowHref: string;
28
- });
29
- makeWorker(): Promise<WebWorkerHandle>;
44
+ private lastWorkerAssignment;
45
+ private workerAssignments;
46
+ private workerPool?;
47
+ private destroyed;
48
+ constructor(pluginManager: PluginManager, config: AnyConfigurationModel, options: WebWorkerRpcDriverOptions);
49
+ /**
50
+ * Free the session on the worker it was assigned to, and drop the assignment
51
+ * so it doesn't accumulate for the life of the driver.
52
+ *
53
+ * A session with no assignment never dispatched anything, so there is nothing
54
+ * cached anywhere to free — and no pool to build in order to find that out.
55
+ */
56
+ freeSession(sessionId: string): Promise<void>;
57
+ destroy(): void;
58
+ private createWorkerPool;
59
+ private getWorkerPool;
60
+ /**
61
+ * Boot the first worker now rather than on the first call, so its bundle and
62
+ * runtime plugins load while the page builds the session. The first session
63
+ * is assigned to that worker.
64
+ */
65
+ warmUp(): void;
66
+ getWorker(sessionId: string): Promise<WorkerHandle>;
67
+ /**
68
+ * Hand a freshly booted worker to whatever plugins want to extend it, and use
69
+ * whatever comes back as the pooled handle.
70
+ *
71
+ * Called from {@link LazyWorker.getWorker} rather than from `makeWorker`,
72
+ * which subclasses override — a seam that skipped the fold would silently
73
+ * un-extend every worker. It answers "what is this worker", not "what is this
74
+ * call", so folding at dispatch needed a WeakMap to stop rebuilding a
75
+ * plugin's wrapper per RPC; once per boot has nothing to memoize.
76
+ */
77
+ extendsWorkers(): boolean;
78
+ extendWorker(worker: WorkerHandle): WorkerHandle;
79
+ protected transport(sessionId: string, rpcMethod: RpcMethodType, serializedArgs: Record<string, unknown>, handles: RpcHandles): Promise<unknown>;
80
+ /**
81
+ * Boot one worker and run the configuration handshake. Overridable so a test
82
+ * can hand the pool a fake handle without a `Worker`; nothing in the app does.
83
+ */
84
+ makeWorker(onHandle?: (handle: WorkerHandle) => void): Promise<WorkerHandle>;
30
85
  }
31
- export {};
@@ -1,77 +1,358 @@
1
- import BaseRpcDriver from "./BaseRpcDriver.js";
2
- import { RpcClient, deserializeError } from "../util/librpc.js";
3
- import { nanoid } from "../util/nanoid.js";
1
+ import { readConfObject } from '../configuration/index.js';
2
+ import { clamp } from '../util/index.js';
3
+ import BaseRpcDriver, { CORE_FREE_RESOURCES } from './BaseRpcDriver.js';
4
+ import RpcClient from './RpcClient.js';
5
+ import { deserializeError } from './serializeError/index.js';
6
+ function detectHardwareConcurrency() {
7
+ // fall back to 1 if navigator.hardwareConcurrency is absent, else clamp()
8
+ // sees NaN and collapses the pool to zero workers
9
+ return typeof navigator === 'undefined'
10
+ ? 1
11
+ : navigator.hardwareConcurrency || 1;
12
+ }
4
13
  class WebWorkerHandle {
5
14
  worker;
6
15
  client;
16
+ // a counter, not a nanoid: the listener map a channel keys into is this
17
+ // handle's own client, so that is the only scope uniqueness is needed in, and
18
+ // the nanoid was a crypto.getRandomValues per reporting call
19
+ channelCount = 0;
7
20
  constructor(worker) {
8
21
  this.worker = worker;
9
22
  this.client = new RpcClient(worker);
23
+ // Listen for worker errors that might not be caught by RpcClient
10
24
  this.client.on('error', error => {
11
25
  console.error('[WebWorker RPC Error]', error);
12
26
  });
13
27
  }
14
28
  destroy() {
29
+ // reject in-flight calls before terminating, else they wait on a reply the
30
+ // dead worker can never send
31
+ this.client.destroy();
15
32
  this.worker.terminate();
16
33
  }
17
- async call(funcName, args, opts) {
18
- const { statusCallback, rpcDriverClassName } = opts;
19
- const channel = `message-${nanoid()}`;
34
+ // lets the pool discard this handle once the worker throws a fatal error
35
+ onError(callback) {
36
+ this.client.on('error', callback);
37
+ }
38
+ // the two halves of {@link WorkerHandle}'s plugin-facing pair
39
+ on(eventName, listener) {
40
+ this.client.on(eventName, listener);
41
+ }
42
+ postMessage(message) {
43
+ this.worker.postMessage(message);
44
+ }
45
+ /**
46
+ * A `channel` only when the caller asked for status, so that "no
47
+ * statusCallback" survives the worker boundary.
48
+ *
49
+ * It did not. The channel was minted unconditionally, and `wrapForRpc` builds
50
+ * the worker's `statusCallback` from whatever channel it is handed — so every
51
+ * method in every worker ran with a live status handle whoever called it had
52
+ * declined, and `MainThreadRpcDriver` (which passes the caller's own
53
+ * `undefined` straight through) answered the same question differently. That
54
+ * asymmetry is the one {@link RpcManager}'s `call` docstring already records
55
+ * in the other direction.
56
+ *
57
+ * The absence is not cosmetic — it is a documented branch. `downloadStatus`
58
+ * hands the reader no `onProgress` without a callback, `createProgressReporter`
59
+ * skips its emit, and every status the worker did send crossed a postMessage
60
+ * to reach a listener that dropped it.
61
+ *
62
+ * The postMessage traffic and the symmetry are the whole case; the read speed
63
+ * is not. `res.bytes()` is the SLOWER of the two reads under ~10MB —
64
+ * agent-docs/measurements/download-read-path.json — and an earlier revision of
65
+ * this comment claimed the opposite because four other places in the tree did.
66
+ */
67
+ async call(funcName, args,
68
+ // defaulted, not required: {@link WorkerHandle} declares it optional, and a
69
+ // `Core-extendWorker` wrapper written against that interface may well call
70
+ // `worker.call(name, args)` — which destructured `undefined` and threw
71
+ opts = {}) {
72
+ const { statusCallback, signal } = opts;
73
+ if (!statusCallback) {
74
+ return this.client.call(funcName, args, signal);
75
+ }
76
+ const channel = `message-${++this.channelCount}`;
77
+ // RpcClient is a generic event emitter (it also carries 'error' events), so
78
+ // its listeners see `unknown`. This channel is dedicated to one method's
79
+ // status emits, which the worker only ever posts as RpcStatus (see
80
+ // wrapForRpc in rpcWorker.ts), so narrowing to RpcStatus here is sound.
20
81
  const listener = (message) => {
21
- statusCallback?.(message);
82
+ statusCallback(message);
22
83
  };
23
84
  this.client.on(channel, listener);
24
85
  try {
25
- const result = await this.client.call(funcName, {
26
- ...args,
27
- channel,
28
- rpcDriverClassName,
29
- });
30
- return result;
86
+ return await this.client.call(funcName, { ...args, channel }, signal);
31
87
  }
32
88
  finally {
33
89
  this.client.off(channel, listener);
34
90
  }
35
91
  }
36
92
  }
93
+ class LazyWorker {
94
+ driver;
95
+ /**
96
+ * The handle this slot booted, and what the pool drives the worker's LIFE on
97
+ * — the error hook and the termination.
98
+ *
99
+ * Kept apart from {@link workerP} because a `Core-extendWorker` plugin only
100
+ * has to forward `call`: `WorkerHandle` makes `onError` and the rest
101
+ * optional, so a conforming wrapper (a spread plus a `call`, which is the
102
+ * obvious way to write one) drops them. Driving the re-boot through such a
103
+ * wrapper means a dead worker is never noticed and the slot never re-boots.
104
+ */
105
+ bootP;
106
+ /** What `Core-extendWorker` returned for it: where calls go. */
107
+ workerP;
108
+ constructor(driver) {
109
+ this.driver = driver;
110
+ }
111
+ async getWorker() {
112
+ if (!this.workerP) {
113
+ let early;
114
+ const booted = this.driver.makeWorker(handle => {
115
+ early = handle;
116
+ });
117
+ this.bootP = booted;
118
+ // A booting worker holds the calls it is sent, so with nothing to extend
119
+ // them a call goes out now rather than when the page gets round to the
120
+ // worker's 'ready'. A boot that fails rejects those calls with the
121
+ // handle. An extended worker is extended once booted, as promised.
122
+ this.workerP =
123
+ early && !this.driver.extendsWorkers()
124
+ ? Promise.resolve(early)
125
+ : // once per booted worker by construction, rather than per dispatch
126
+ // behind a memo
127
+ booted.then(worker => this.driver.extendWorker(worker));
128
+ // drop this slot so the next getWorker re-boots, whether the boot failed
129
+ // or the booted worker later died (a dead worker never replies)
130
+ const invalidate = () => {
131
+ if (this.bootP === booted) {
132
+ this.bootP = undefined;
133
+ this.workerP = undefined;
134
+ }
135
+ };
136
+ booted
137
+ .then(worker => {
138
+ worker.onError?.(() => {
139
+ invalidate();
140
+ worker.destroy();
141
+ });
142
+ })
143
+ .catch(invalidate);
144
+ }
145
+ return this.workerP;
146
+ }
147
+ destroy() {
148
+ // terminate the underlying worker once it resolves; a worker that never
149
+ // booted (rejected promise) has nothing to terminate, so swallow that
150
+ this.bootP
151
+ ?.then(worker => {
152
+ worker.destroy();
153
+ })
154
+ .catch(() => { });
155
+ this.bootP = undefined;
156
+ this.workerP = undefined;
157
+ }
158
+ /**
159
+ * Drop a session's cached adapters on this slot's worker, and never boot one
160
+ * to do it. A slot that never booted has no cache to free, and booting one
161
+ * there costs a whole worker bundle and every runtime plugin to say so.
162
+ *
163
+ * Through the extended handle, because it is a `call`: a plugin that wraps
164
+ * calls should see this one.
165
+ *
166
+ * Awaited rather than fire-and-forget, because a caller can be waiting to
167
+ * know the adapter is gone; a slot still booting frees once it lands.
168
+ */
169
+ async freeSession(sessionId) {
170
+ const worker = await this.workerP?.catch(() => undefined);
171
+ await worker?.call(CORE_FREE_RESOURCES, { sessionId });
172
+ }
173
+ }
174
+ /**
175
+ * Runs RPC methods in a pool of lazily-booted web workers, with our own
176
+ * state-group-aware round-robin assignment (one sticky worker per session) so a
177
+ * session's calls land on the same worker and can share cached adapters.
178
+ *
179
+ * The pool is here rather than in a `WorkerPoolRpcDriver` above it: that base
180
+ * abstracted `makeWorker`, which has one implementation. It is a plain
181
+ * overridable method now, which is all the seam was ever used for. ADR-086.
182
+ */
37
183
  export default class WebWorkerRpcDriver extends BaseRpcDriver {
38
- workerBootConfiguration;
184
+ options;
39
185
  name = 'WebWorkerRpcDriver';
40
- makeWorkerInstance;
41
- constructor(args, workerBootConfiguration) {
42
- super(args);
43
- this.workerBootConfiguration = workerBootConfiguration;
44
- this.makeWorkerInstance = args.makeWorkerInstance;
45
- }
46
- async makeWorker() {
47
- const instance = this.makeWorkerInstance();
186
+ lastWorkerAssignment = -1;
187
+ // sessionId -> worker number
188
+ workerAssignments = new Map();
189
+ workerPool;
190
+ // `destroy` is terminal: `getWorkerPool` refuses rather than letting its `??=`
191
+ // build a second pool for a driver whose teardown already ran. ADR-086.
192
+ destroyed = false;
193
+ constructor(pluginManager, config, options) {
194
+ super(pluginManager, config);
195
+ this.options = options;
196
+ }
197
+ /**
198
+ * Free the session on the worker it was assigned to, and drop the assignment
199
+ * so it doesn't accumulate for the life of the driver.
200
+ *
201
+ * A session with no assignment never dispatched anything, so there is nothing
202
+ * cached anywhere to free — and no pool to build in order to find that out.
203
+ */
204
+ async freeSession(sessionId) {
205
+ const workerNumber = this.workerAssignments.get(sessionId);
206
+ this.workerAssignments.delete(sessionId);
207
+ if (workerNumber !== undefined) {
208
+ await this.workerPool?.[workerNumber]?.freeSession(sessionId);
209
+ }
210
+ }
211
+ // terminate every pooled worker and reset assignment bookkeeping; call when
212
+ // discarding the driver so its worker threads don't outlive it
213
+ destroy() {
214
+ this.destroyed = true;
215
+ for (const worker of this.workerPool ?? []) {
216
+ worker.destroy();
217
+ }
218
+ this.workerPool = undefined;
219
+ this.workerAssignments.clear();
220
+ this.lastWorkerAssignment = -1;
221
+ }
222
+ createWorkerPool() {
223
+ // workerCount 0 (the config default) means "decide from hardware"
224
+ const workerCount = readConfObject(this.config, 'workerCount') ||
225
+ clamp(detectHardwareConcurrency() - 1, 1, 5);
226
+ return Array.from({ length: workerCount }, () => new LazyWorker(this));
227
+ }
228
+ getWorkerPool() {
229
+ if (this.destroyed) {
230
+ throw new Error(`${this.name} was destroyed`);
231
+ }
232
+ return (this.workerPool ??= this.createWorkerPool());
233
+ }
234
+ /**
235
+ * Boot the first worker now rather than on the first call, so its bundle and
236
+ * runtime plugins load while the page builds the session. The first session
237
+ * is assigned to that worker.
238
+ */
239
+ warmUp() {
240
+ if (!this.destroyed) {
241
+ this.getWorkerPool()[0]
242
+ ?.getWorker()
243
+ .catch(() => { });
244
+ }
245
+ }
246
+ async getWorker(sessionId) {
247
+ const workers = this.getWorkerPool();
248
+ let workerNumber = this.workerAssignments.get(sessionId);
249
+ if (workerNumber === undefined) {
250
+ workerNumber = (this.lastWorkerAssignment + 1) % workers.length;
251
+ this.workerAssignments.set(sessionId, workerNumber);
252
+ this.lastWorkerAssignment = workerNumber;
253
+ }
254
+ return workers[workerNumber].getWorker();
255
+ }
256
+ /**
257
+ * Hand a freshly booted worker to whatever plugins want to extend it, and use
258
+ * whatever comes back as the pooled handle.
259
+ *
260
+ * Called from {@link LazyWorker.getWorker} rather than from `makeWorker`,
261
+ * which subclasses override — a seam that skipped the fold would silently
262
+ * un-extend every worker. It answers "what is this worker", not "what is this
263
+ * call", so folding at dispatch needed a WeakMap to stop rebuilding a
264
+ * plugin's wrapper per RPC; once per boot has nothing to memoize.
265
+ */
266
+ extendsWorkers() {
267
+ return (this.pluginManager.extensionPointCallbackCount('Core-extendWorker') > 0);
268
+ }
269
+ extendWorker(worker) {
270
+ return this.pluginManager.evaluateExtensionPoint(
271
+ /** #extensionPoint Core-extendWorker | sync | Take a booted RPC web worker: subscribe to the events it emits, post to it, or wrap its `call`. Fired once per booted worker, not per call */
272
+ 'Core-extendWorker', worker);
273
+ }
274
+ // get this session's sticky worker and hand off the already-serialized args
275
+ async transport(sessionId, rpcMethod, serializedArgs, handles) {
276
+ const worker = await this.getWorker(sessionId);
277
+ return worker.call(rpcMethod.name, serializedArgs, handles);
278
+ }
279
+ /**
280
+ * Boot one worker and run the configuration handshake. Overridable so a test
281
+ * can hand the pool a fake handle without a `Worker`; nothing in the app does.
282
+ */
283
+ async makeWorker(onHandle) {
284
+ // one RpcClient per worker so we can do our own state-group-aware load
285
+ // balancing across the pool
286
+ const instance = this.options.makeWorkerInstance();
48
287
  const handle = new WebWorkerHandle(instance);
49
288
  const isSafari = /^((?!chrome|android).)*safari/i.test(navigator.userAgent);
50
289
  if (isSafari) {
290
+ // xref https://github.com/GMOD/jbrowse-components/issues/3245
291
+ // eslint-disable-next-line no-console
51
292
  console.log('console logging the webworker handle avoids the track going into an infinite loading state, this is a hacky workaround for safari', instance);
52
293
  }
294
+ // send the worker its boot configuration using info from the pluginManager
53
295
  return new Promise((resolve, reject) => {
54
- const listener = (e) => {
296
+ const cleanup = () => {
297
+ instance.removeEventListener('message', onMessage);
298
+ instance.removeEventListener('error', onError);
299
+ };
300
+ // the pool discards this slot and re-boots on the next call, so terminate
301
+ // the half-booted worker rather than orphaning its thread
302
+ const fail = (error) => {
303
+ cleanup();
304
+ handle.destroy();
305
+ reject(error);
306
+ };
307
+ // The worker waits in receiveConfiguration(), which has no timeout, so an
308
+ // unclonable boot configuration has to fail the boot rather than leave
309
+ // both sides waiting.
310
+ const sendConfig = () => {
311
+ try {
312
+ const { plugins, windowHref, numberGrouping } = this.options;
313
+ instance.postMessage({
314
+ message: 'config',
315
+ config: { plugins, windowHref, numberGrouping },
316
+ });
317
+ }
318
+ catch (e) {
319
+ fail(new Error(`could not send the worker its boot configuration`, {
320
+ cause: e,
321
+ }));
322
+ }
323
+ };
324
+ const onMessage = (e) => {
55
325
  switch (e.data.message) {
56
326
  case 'ready': {
327
+ cleanup();
57
328
  resolve(handle);
58
- instance.removeEventListener('message', listener);
59
329
  break;
60
330
  }
61
331
  case 'readyForConfig': {
62
- instance.postMessage({
63
- message: 'config',
64
- config: this.workerBootConfiguration,
65
- });
332
+ sendConfig();
66
333
  break;
67
334
  }
68
335
  case 'error': {
69
- reject(deserializeError(e.data.error));
336
+ fail(deserializeError(e.data.error));
70
337
  break;
71
338
  }
339
+ // No default
72
340
  }
73
341
  };
74
- instance.addEventListener('message', listener);
342
+ // a worker that throws while loading its script posts no message, so
343
+ // reject on the raw ErrorEvent too, else the boot promise hangs forever
344
+ const onError = (e) => {
345
+ fail(new Error(e.message || 'worker failed to load'));
346
+ };
347
+ instance.addEventListener('message', onMessage);
348
+ instance.addEventListener('error', onError);
349
+ // A dedicated worker holds what it is sent until its script has run, and
350
+ // receiveConfiguration listens from that run, so the config can go now,
351
+ // and a worker created before this driver needs no readyForConfig. It is
352
+ // sent again on readyForConfig for a worker whose startup awaits chunks
353
+ // and so would drop this one; the worker keeps the first.
354
+ sendConfig();
355
+ onHandle?.(handle);
75
356
  });
76
357
  }
77
358
  }
@@ -0,0 +1,64 @@
1
+ import type { StatusCallback } from '../util/progress.ts';
2
+ import type { AugmentedRegion } from '../util/types/data.ts';
3
+ /**
4
+ * Which question a byte budget asks of a region set: the gate's per-region
5
+ * budget, or the save dialog's bound on the whole download.
6
+ */
7
+ export type ByteEstimateScope = 'largestRegion' | 'wholeRequest';
8
+ /**
9
+ * The one spelling of a gated feature RPC's budget argument: the number the
10
+ * worker measures against, undefined when the gate declined to act and nothing
11
+ * is measured. A call-site argument, never part of `rpcProps`, because it
12
+ * swings at 20kb and on force-load.
13
+ */
14
+ export interface GatedFetchArgs {
15
+ byteLimit?: number;
16
+ }
17
+ export interface ByteMeasurableAdapter {
18
+ getRegionByteSize: (regions: AugmentedRegion[], opts?: {
19
+ signal?: AbortSignal;
20
+ statusCallback?: StatusCallback;
21
+ }) => Promise<number | undefined>;
22
+ }
23
+ /**
24
+ * What a gated fetch RPC answers instead of a payload when a region is over
25
+ * budget on either axis, carrying everything measured on the way: the byte
26
+ * stage runs first, so a density refusal still has `bytes`.
27
+ */
28
+ export interface RegionTooLargeResult {
29
+ regionTooLarge: true;
30
+ featureCount?: number;
31
+ bytes?: number;
32
+ /** `bytes` is the max over the regions that reported — {@link measurementPartial} */
33
+ partial?: boolean;
34
+ }
35
+ export declare function isRegionRefused(result: unknown): result is RegionTooLargeResult;
36
+ /** Undefined, never 0, when no region could be measured. */
37
+ export declare function largestRegionBytes(perRegion: (number | undefined)[]): number | undefined;
38
+ /** A non-positive declared limit means "no opinion" (htsget reports 0). */
39
+ export declare function adapterByteLimit(declared: unknown, fallback: number): number;
40
+ export declare function overByteBudget(bytes: number | undefined, byteLimit: number | undefined): bytes is number;
41
+ /** The bytes a fetch result reports, payload or refusal; absent means unmeasured. */
42
+ export declare function measuredBytes(result: unknown): number | undefined;
43
+ /**
44
+ * Whether a result's `bytes` covers the whole region set it was asked about. A
45
+ * fan-out that stops at its first refusal reports whichever regions won the
46
+ * race, and `nextByteEstimate` takes no zoom evidence from one.
47
+ */
48
+ export declare function measurementPartial(result: unknown): boolean;
49
+ /**
50
+ * The first await of every gated feature fetch: each region's index-only byte
51
+ * estimate, judged by the largest because the budget is per region. `bytes`
52
+ * comes back either way; when `tooLarge` is set the caller returns it and
53
+ * fetches nothing. No budget means no measurement.
54
+ */
55
+ export declare function measureRegionBytes({ dataAdapter, regions, byteLimit, signal, statusCallback, }: {
56
+ dataAdapter: ByteMeasurableAdapter;
57
+ regions: AugmentedRegion[];
58
+ byteLimit: number | undefined;
59
+ signal?: AbortSignal;
60
+ statusCallback?: StatusCallback;
61
+ }): Promise<{
62
+ bytes?: number;
63
+ tooLarge?: RegionTooLargeResult;
64
+ }>;
@@ -0,0 +1,61 @@
1
+ import { checkAbortSignal } from '../util/aborting.js';
2
+ import { updateStatus } from '../util/progress.js';
3
+ export function isRegionRefused(result) {
4
+ return (typeof result === 'object' && result !== null && 'regionTooLarge' in result);
5
+ }
6
+ /** Undefined, never 0, when no region could be measured. */
7
+ export function largestRegionBytes(perRegion) {
8
+ let largest;
9
+ for (const bytes of perRegion) {
10
+ if (bytes !== undefined && (largest === undefined || bytes > largest)) {
11
+ largest = bytes;
12
+ }
13
+ }
14
+ return largest;
15
+ }
16
+ /** A non-positive declared limit means "no opinion" (htsget reports 0). */
17
+ export function adapterByteLimit(declared, fallback) {
18
+ return typeof declared === 'number' && declared > 0 ? declared : fallback;
19
+ }
20
+ export function overByteBudget(bytes, byteLimit) {
21
+ return bytes !== undefined && byteLimit !== undefined && bytes > byteLimit;
22
+ }
23
+ /** The bytes a fetch result reports, payload or refusal; absent means unmeasured. */
24
+ export function measuredBytes(result) {
25
+ return typeof result === 'object' &&
26
+ result !== null &&
27
+ 'bytes' in result &&
28
+ typeof result.bytes === 'number'
29
+ ? result.bytes
30
+ : undefined;
31
+ }
32
+ /**
33
+ * Whether a result's `bytes` covers the whole region set it was asked about. A
34
+ * fan-out that stops at its first refusal reports whichever regions won the
35
+ * race, and `nextByteEstimate` takes no zoom evidence from one.
36
+ */
37
+ export function measurementPartial(result) {
38
+ return (typeof result === 'object' &&
39
+ result !== null &&
40
+ 'partial' in result &&
41
+ result.partial === true);
42
+ }
43
+ /**
44
+ * The first await of every gated feature fetch: each region's index-only byte
45
+ * estimate, judged by the largest because the budget is per region. `bytes`
46
+ * comes back either way; when `tooLarge` is set the caller returns it and
47
+ * fetches nothing. No budget means no measurement.
48
+ */
49
+ export async function measureRegionBytes({ dataAdapter, regions, byteLimit, signal, statusCallback, }) {
50
+ if (byteLimit === undefined) {
51
+ return {};
52
+ }
53
+ const bytes = largestRegionBytes(await updateStatus('Downloading index', statusCallback, () => Promise.all(regions.map(region => dataAdapter.getRegionByteSize([region], {
54
+ signal,
55
+ statusCallback,
56
+ })))));
57
+ checkAbortSignal(signal);
58
+ return overByteBudget(bytes, byteLimit)
59
+ ? { bytes, tooLarge: { regionTooLarge: true, bytes } }
60
+ : { bytes };
61
+ }
@@ -1,9 +1,17 @@
1
+ /**
2
+ * #config RpcOptions
3
+ * #category root
4
+ */
1
5
  declare const _default: import("../configuration/configurationSchema.ts").ConfigurationSchemaType<{
2
- defaultDriver: {
3
- type: string;
4
- description: string;
6
+ readonly defaultDriver: {
7
+ type: "string";
8
+ } & {
5
9
  defaultValue: string;
6
10
  };
7
- 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]>;
8
- }, import("../configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
11
+ readonly workerCount: {
12
+ type: "number";
13
+ } & {
14
+ defaultValue: number;
15
+ };
16
+ }, import("../configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined, undefined, import("../configuration/requirements.ts").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
9
17
  export default _default;