@jbrowse/core 4.3.0 → 5.0.0-beta.2

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 (1140) hide show
  1. package/README.md +822 -0
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +13 -3
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +33 -22
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +8 -3
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +117 -19
  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 -2
  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 +1 -1
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +12 -5
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +28 -17
  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 +6 -4
  19. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +46 -30
  20. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
  21. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
  22. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
  23. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
  24. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
  25. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +17 -0
  26. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +1 -1
  27. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +3 -9
  28. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +3 -2
  29. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +3 -3
  30. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
  31. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
  32. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +2 -1
  33. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +19 -13
  34. package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +5 -4
  35. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +8 -1
  36. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +32 -10
  37. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
  38. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
  39. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
  40. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +62 -24
  41. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
  42. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
  43. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +1 -1
  44. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
  45. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
  46. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
  47. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
  48. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
  49. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
  50. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
  51. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
  52. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
  53. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
  54. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
  55. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
  56. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
  57. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
  58. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
  59. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
  60. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
  61. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
  62. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
  63. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
  64. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
  65. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
  66. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +18 -0
  67. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
  68. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
  69. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
  70. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +50 -63
  71. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +62 -59
  72. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
  73. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
  74. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
  75. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
  76. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
  77. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
  78. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
  79. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
  80. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
  81. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
  82. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
  83. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
  84. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
  85. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
  86. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
  87. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
  88. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +1 -1
  89. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +7 -7
  90. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
  91. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
  92. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
  93. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
  94. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
  95. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
  96. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
  97. package/esm/BaseFeatureWidget/configSchema.js +1 -1
  98. package/esm/BaseFeatureWidget/formatDetails.d.ts +38 -0
  99. package/esm/BaseFeatureWidget/formatDetails.js +103 -0
  100. package/esm/BaseFeatureWidget/index.d.ts +3 -1
  101. package/esm/BaseFeatureWidget/index.js +2 -2
  102. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +80 -62
  103. package/esm/BaseFeatureWidget/stateModelFactory.js +128 -29
  104. package/esm/BaseFeatureWidget/types.d.ts +4 -3
  105. package/esm/BaseFeatureWidget/util.d.ts +4 -29
  106. package/esm/BaseFeatureWidget/util.js +20 -84
  107. package/esm/CorePlugin.js +11 -6
  108. package/esm/PhasedScheduler.d.ts +4 -2
  109. package/esm/PhasedScheduler.js +18 -2
  110. package/esm/Plugin.d.ts +6 -1
  111. package/esm/Plugin.js +7 -0
  112. package/esm/PluginLoader.d.ts +41 -40
  113. package/esm/PluginLoader.js +206 -78
  114. package/esm/PluginManager.d.ts +421 -55
  115. package/esm/PluginManager.js +461 -89
  116. package/esm/ReExports/BaseFeatureDetails.js +7 -6
  117. package/esm/ReExports/MuiDataGridReExports.d.ts +2 -2
  118. package/esm/ReExports/MuiDataGridReExports.js +58 -130
  119. package/esm/ReExports/MuiReExports.d.ts +3 -134
  120. package/esm/ReExports/MuiReExports.js +43 -16
  121. package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
  122. package/esm/ReExports/MuiStylesReExports.js +55 -0
  123. package/esm/ReExports/index.js +1 -1
  124. package/esm/ReExports/lazify.d.ts +2 -2
  125. package/esm/ReExports/lazify.js +16 -3
  126. package/esm/ReExports/list.js +54 -229
  127. package/esm/ReExports/modules.js +62 -93
  128. package/esm/ReExports/muiComponentNames.d.ts +18 -0
  129. package/esm/ReExports/muiComponentNames.js +130 -0
  130. package/esm/ReExports/publicUtil.d.ts +1 -0
  131. package/esm/ReExports/publicUtil.js +28 -0
  132. package/esm/ReExports/registry.d.ts +2 -0
  133. package/esm/ReExports/registry.js +28 -0
  134. package/esm/ReExports/sharedModules.d.ts +96 -0
  135. package/esm/ReExports/sharedModules.js +59 -0
  136. package/esm/ReExports/uiStub.d.ts +1 -0
  137. package/esm/ReExports/uiStub.js +13 -0
  138. package/esm/ReExports/workerModules.d.ts +2 -0
  139. package/esm/ReExports/workerModules.js +10 -0
  140. package/esm/TextSearch/BaseResults.d.ts +20 -21
  141. package/esm/TextSearch/BaseResults.js +8 -33
  142. package/esm/TextSearch/TextSearchManager.d.ts +14 -34
  143. package/esm/TextSearch/TextSearchManager.js +87 -34
  144. package/esm/assemblyManager/assembly.d.ts +307 -34
  145. package/esm/assemblyManager/assembly.js +551 -262
  146. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  147. package/esm/assemblyManager/assemblyAdapters.js +18 -0
  148. package/esm/assemblyManager/assemblyConfigSchema.d.ts +192 -17
  149. package/esm/assemblyManager/assemblyConfigSchema.js +213 -19
  150. package/esm/assemblyManager/assemblyManager.d.ts +711 -303
  151. package/esm/assemblyManager/assemblyManager.js +351 -46
  152. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +32 -0
  153. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +85 -0
  154. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  155. package/esm/assemblyManager/geneticCodes.js +47 -0
  156. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +9 -0
  157. package/esm/assemblyManager/getSequenceAdapterConfig.js +12 -0
  158. package/esm/assemblyManager/index.d.ts +1 -1
  159. package/esm/assemblyManager/index.js +2 -2
  160. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  161. package/esm/assemblyManager/loadRefNameMap.js +80 -0
  162. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  163. package/esm/assemblyManager/refNameColors.js +32 -0
  164. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  165. package/esm/assemblyManager/refNameMaps.js +87 -0
  166. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  167. package/esm/assemblyManager/refNameMismatch.js +66 -0
  168. package/esm/checkPlugins.d.ts +11 -0
  169. package/esm/checkPlugins.js +77 -0
  170. package/esm/configuration/configurationSchema.d.ts +122 -20
  171. package/esm/configuration/configurationSchema.js +374 -140
  172. package/esm/configuration/configurationSlot.d.ts +283 -30
  173. package/esm/configuration/configurationSlot.js +205 -226
  174. package/esm/configuration/formatAboutConfigSchema.d.ts +55 -0
  175. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  176. package/esm/configuration/formatDetailsConfigSchema.d.ts +80 -0
  177. package/esm/configuration/formatDetailsConfigSchema.js +90 -0
  178. package/esm/configuration/fullConfSnapshot.d.ts +28 -0
  179. package/esm/configuration/fullConfSnapshot.js +66 -0
  180. package/esm/configuration/getConf.d.ts +88 -0
  181. package/esm/configuration/getConf.js +74 -0
  182. package/esm/configuration/index.d.ts +19 -3
  183. package/esm/configuration/index.js +19 -2
  184. package/esm/configuration/mergeFormatCallbacks.d.ts +15 -0
  185. package/esm/configuration/mergeFormatCallbacks.js +24 -0
  186. package/esm/configuration/promotableDefaults.d.ts +199 -0
  187. package/esm/configuration/promotableDefaults.js +332 -0
  188. package/esm/configuration/promotablePin.d.ts +55 -0
  189. package/esm/configuration/promotableResolve.d.ts +108 -0
  190. package/esm/configuration/promotableResolve.js +117 -0
  191. package/esm/configuration/promotableSlots.d.ts +12 -0
  192. package/esm/configuration/promotableSlots.js +45 -0
  193. package/esm/configuration/readConfObject.d.ts +56 -0
  194. package/esm/configuration/readConfObject.js +161 -0
  195. package/esm/configuration/schemaRegistry.d.ts +35 -0
  196. package/esm/configuration/schemaRegistry.js +50 -0
  197. package/esm/configuration/schemaTypes.d.ts +23 -0
  198. package/esm/configuration/schemaTypes.js +94 -0
  199. package/esm/configuration/slotFacade.d.ts +82 -0
  200. package/esm/configuration/slotFacade.js +89 -0
  201. package/esm/configuration/slotShape.d.ts +12 -0
  202. package/esm/configuration/slotShape.js +84 -0
  203. package/esm/configuration/slotValueUtils.d.ts +17 -0
  204. package/esm/configuration/slotValueUtils.js +25 -0
  205. package/esm/configuration/tabixIndexFields.d.ts +44 -0
  206. package/esm/configuration/tabixIndexFields.js +45 -0
  207. package/esm/configuration/tabixShorthand.d.ts +34 -0
  208. package/esm/configuration/tabixShorthand.js +45 -0
  209. package/esm/configuration/types.d.ts +170 -7
  210. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +24 -10
  211. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +23 -15
  212. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +132 -7
  213. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +136 -25
  214. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  215. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  216. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  217. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  218. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  219. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  220. package/esm/data_adapters/BaseAdapter/featureDensity.d.ts +29 -0
  221. package/esm/data_adapters/BaseAdapter/featureDensity.js +17 -0
  222. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  223. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  224. package/esm/data_adapters/BaseAdapter/index.d.ts +7 -4
  225. package/esm/data_adapters/BaseAdapter/index.js +6 -5
  226. package/esm/data_adapters/BaseAdapter/stats.d.ts +37 -5
  227. package/esm/data_adapters/BaseAdapter/stats.js +89 -24
  228. package/esm/data_adapters/BaseAdapter/types.d.ts +11 -8
  229. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  230. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  231. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  232. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  233. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +4 -4
  234. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +36 -4
  235. package/esm/data_adapters/CytobandAdapter/configSchema.js +46 -2
  236. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  237. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  238. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  239. package/esm/data_adapters/dataAdapterCache.d.ts +35 -1
  240. package/esm/data_adapters/dataAdapterCache.js +62 -22
  241. package/esm/data_adapters/getFeatureAdapter.d.ts +22 -0
  242. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  243. package/esm/data_adapters/getSequenceSubAdapter.d.ts +21 -0
  244. package/esm/data_adapters/getSequenceSubAdapter.js +44 -0
  245. package/esm/pluggableElementTypes/AdapterType.d.ts +52 -2
  246. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  247. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  248. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  249. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  250. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  251. package/esm/pluggableElementTypes/DisplayType.d.ts +19 -10
  252. package/esm/pluggableElementTypes/DisplayType.js +53 -5
  253. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  254. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +13 -0
  255. package/esm/pluggableElementTypes/PluggableElementBase.js +13 -0
  256. package/esm/pluggableElementTypes/RpcMethodType.d.ts +132 -12
  257. package/esm/pluggableElementTypes/RpcMethodType.js +263 -98
  258. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +19 -9
  259. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  260. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  261. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  262. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  263. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  264. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +3 -3
  265. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  266. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  267. package/esm/pluggableElementTypes/TrackType.js +1 -1
  268. package/esm/pluggableElementTypes/ViewType.d.ts +27 -3
  269. package/esm/pluggableElementTypes/ViewType.js +84 -4
  270. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  271. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  272. package/esm/pluggableElementTypes/addMenuItems.d.ts +87 -0
  273. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  274. package/esm/pluggableElementTypes/extendElementType.d.ts +30 -0
  275. package/esm/pluggableElementTypes/extendElementType.js +73 -0
  276. package/esm/pluggableElementTypes/index.d.ts +7 -7
  277. package/esm/pluggableElementTypes/index.js +24 -14
  278. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +70 -15
  279. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  280. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +646 -84
  281. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +241 -60
  282. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +216 -35
  283. package/esm/pluggableElementTypes/models/BaseTrackModel.js +365 -83
  284. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +216 -16
  285. package/esm/pluggableElementTypes/models/BaseViewModel.js +150 -16
  286. package/esm/pluggableElementTypes/models/HighlightsMixin.d.ts +51 -0
  287. package/esm/pluggableElementTypes/models/HighlightsMixin.js +78 -0
  288. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +163 -29
  289. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  290. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +177 -0
  291. package/esm/pluggableElementTypes/models/assertDisplayContract.js +239 -0
  292. package/esm/pluggableElementTypes/models/baseConnectionConfig.d.ts +22 -8
  293. package/esm/pluggableElementTypes/models/baseConnectionConfig.js +18 -2
  294. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +39 -20
  295. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.js +23 -2
  296. package/esm/pluggableElementTypes/models/baseTrackConfig.d.ts +181 -65
  297. package/esm/pluggableElementTypes/models/baseTrackConfig.js +191 -89
  298. package/esm/pluggableElementTypes/models/components/SaveTrackData.d.ts +3 -8
  299. package/esm/pluggableElementTypes/models/components/SaveTrackData.js +113 -139
  300. package/esm/pluggableElementTypes/models/components/fetchTrackData.d.ts +55 -0
  301. package/esm/pluggableElementTypes/models/components/fetchTrackData.js +83 -0
  302. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.d.ts +40 -0
  303. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.js +115 -0
  304. package/esm/pluggableElementTypes/models/index.d.ts +6 -3
  305. package/esm/pluggableElementTypes/models/index.js +10 -8
  306. package/esm/pluggableElementTypes/models/migrateTrackConfig.d.ts +34 -0
  307. package/esm/pluggableElementTypes/models/migrateTrackConfig.js +54 -0
  308. package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.js +75 -7
  309. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.d.ts +9 -3
  310. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +153 -103
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  1024. package/esm/util/usePanZoom.d.ts +75 -0
  1025. package/esm/util/usePanZoom.js +175 -0
  1026. package/esm/util/usePanelVirtualScroll.d.ts +37 -0
  1027. package/esm/util/usePanelVirtualScroll.js +42 -0
  1028. package/esm/util/usePointerDrag.d.ts +37 -0
  1029. package/esm/util/usePointerDrag.js +61 -0
  1030. package/esm/util/useRafCommit.d.ts +4 -0
  1031. package/esm/util/useRafCommit.js +50 -0
  1032. package/esm/util/useResizeDrag.d.ts +91 -0
  1033. package/esm/util/useResizeDrag.js +105 -0
  1034. package/esm/util/useRowVirtualScroll.d.ts +32 -0
  1035. package/esm/util/useRowVirtualScroll.js +63 -0
  1036. package/esm/util/useVirtualScrollWheel.d.ts +7 -0
  1037. package/esm/util/useVirtualScrollWheel.js +108 -0
  1038. package/esm/util/viewStatus.d.ts +81 -0
  1039. package/esm/util/viewStatus.js +37 -0
  1040. package/esm/util/virtualRange.d.ts +36 -0
  1041. package/esm/util/virtualRange.js +26 -0
  1042. package/esm/util/webStorage.d.ts +26 -0
  1043. package/esm/util/webStorage.js +92 -0
  1044. package/esm/util/wheelZoom.d.ts +59 -0
  1045. package/esm/util/wheelZoom.js +231 -0
  1046. package/esm/util/whenViewSettled.d.ts +40 -0
  1047. package/esm/util/whenViewSettled.js +41 -0
  1048. package/esm/util/withFeatureDetails.d.ts +34 -0
  1049. package/esm/util/withFeatureDetails.js +59 -0
  1050. package/esm/util/withLaunchInput.d.ts +123 -0
  1051. package/esm/util/withLaunchInput.js +228 -0
  1052. package/package.json +243 -820
  1053. package/esm/ReExports/DataGrid.d.ts +0 -1
  1054. package/esm/ReExports/DataGrid.js +0 -1
  1055. package/esm/configuration/util.d.ts +0 -10
  1056. package/esm/configuration/util.js +0 -123
  1057. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
  1058. package/esm/data_adapters/util.d.ts +0 -1
  1059. package/esm/data_adapters/util.js +0 -6
  1060. package/esm/pluggableElementTypes/GlyphType.d.ts +0 -43
  1061. package/esm/pluggableElementTypes/GlyphType.js +0 -18
  1062. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +0 -5
  1063. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +0 -17
  1064. package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +0 -52
  1065. package/esm/pluggableElementTypes/renderers/BoxRendererType.js +0 -78
  1066. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +0 -4
  1067. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +0 -4
  1068. package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -58
  1069. package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +0 -77
  1070. package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +0 -31
  1071. package/esm/pluggableElementTypes/renderers/LayoutSession.js +0 -40
  1072. package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
  1073. package/esm/pluggableElementTypes/renderers/RendererType.js +0 -20
  1074. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +0 -58
  1075. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.js +0 -108
  1076. package/esm/pluggableElementTypes/renderers/index.d.ts +0 -6
  1077. package/esm/pluggableElementTypes/renderers/index.js +0 -6
  1078. package/esm/pluggableElementTypes/renderers/util.d.ts +0 -3
  1079. package/esm/pluggableElementTypes/renderers/util.js +0 -14
  1080. package/esm/rpc/baseRpcConfig.d.ts +0 -8
  1081. package/esm/rpc/baseRpcConfig.js +0 -10
  1082. package/esm/rpc/mainThreadRpcConfig.d.ts +0 -8
  1083. package/esm/rpc/mainThreadRpcConfig.js +0 -8
  1084. package/esm/rpc/methods/CoreGetFeatureDensityStats.d.ts +0 -17
  1085. package/esm/rpc/methods/CoreGetFeatureDensityStats.js +0 -25
  1086. package/esm/rpc/methods/CoreGetFeatureDetails.d.ts +0 -11
  1087. package/esm/rpc/methods/CoreGetFeatureDetails.js +0 -24
  1088. package/esm/rpc/methods/CoreGetFileInfo.d.ts +0 -9
  1089. package/esm/rpc/methods/CoreGetFileInfo.js +0 -15
  1090. package/esm/rpc/methods/CoreRender.d.ts +0 -14
  1091. package/esm/rpc/methods/CoreRender.js +0 -40
  1092. package/esm/rpc/methods/CoreSaveFeatureData.d.ts +0 -16
  1093. package/esm/rpc/methods/CoreSaveFeatureData.js +0 -32
  1094. package/esm/rpc/methods/util.d.ts +0 -15
  1095. package/esm/rpc/methods/util.js +0 -7
  1096. package/esm/rpc/webWorkerRpcConfig.d.ts +0 -8
  1097. package/esm/rpc/webWorkerRpcConfig.js +0 -8
  1098. package/esm/ui/MenuButton.d.ts +0 -1
  1099. package/esm/ui/MenuButton.js +0 -1
  1100. package/esm/ui/MenuItems.d.ts +0 -15
  1101. package/esm/ui/MenuItems.js +0 -59
  1102. package/esm/ui/useEvent.d.ts +0 -1
  1103. package/esm/ui/useEvent.js +0 -10
  1104. package/esm/util/blobToDataURL.d.ts +0 -1
  1105. package/esm/util/blobToDataURL.js +0 -14
  1106. package/esm/util/compositeMap.d.ts +0 -11
  1107. package/esm/util/compositeMap.js +0 -59
  1108. package/esm/util/flatqueue/index.d.ts +0 -11
  1109. package/esm/util/flatqueue/index.js +0 -61
  1110. package/esm/util/layouts/BaseLayout.d.ts +0 -30
  1111. package/esm/util/layouts/MultiLayout.d.ts +0 -12
  1112. package/esm/util/layouts/MultiLayout.js +0 -40
  1113. package/esm/util/layouts/PileupLayout.d.ts +0 -41
  1114. package/esm/util/layouts/PileupLayout.js +0 -202
  1115. package/esm/util/layouts/PrecomputedLayout.d.ts +0 -30
  1116. package/esm/util/layouts/PrecomputedLayout.js +0 -71
  1117. package/esm/util/layouts/SceneGraph.d.ts +0 -31
  1118. package/esm/util/layouts/SceneGraph.js +0 -121
  1119. package/esm/util/makeAbortableReaction.d.ts +0 -3
  1120. package/esm/util/makeAbortableReaction.js +0 -47
  1121. package/esm/util/map-obj/index.d.ts +0 -13
  1122. package/esm/util/map-obj/index.js +0 -92
  1123. package/esm/util/nextTick.d.ts +0 -1
  1124. package/esm/util/nextTick.js +0 -3
  1125. package/esm/util/offscreenCanvasGetSerializingSvg.d.ts +0 -5
  1126. package/esm/util/offscreenCanvasGetSerializingSvg.js +0 -9
  1127. package/esm/util/offscreenCanvasUtils.d.ts +0 -12
  1128. package/esm/util/offscreenCanvasUtils.js +0 -19
  1129. package/esm/util/renderToAbstractCanvas.d.ts +0 -17
  1130. package/esm/util/renderToAbstractCanvas.js +0 -53
  1131. package/esm/util/transferables.d.ts +0 -2
  1132. package/esm/util/transferables.js +0 -35
  1133. package/esm/util/tss-react/mui/index.d.ts +0 -1
  1134. package/esm/util/tss-react/mui/index.js +0 -1
  1135. package/esm/util/tss-react/mui/mui.d.ts +0 -10
  1136. package/esm/util/tss-react/mui/mui.js +0 -5
  1137. package/esm/util/when.d.ts +0 -1
  1138. package/esm/util/when.js +0 -1
  1139. /package/esm/{data_adapters/BaseAdapter/BaseOptions.js → configuration/promotablePin.js} +0 -0
  1140. /package/esm/{util/layouts/BaseLayout.js → data_adapters/BaseAdapter/CytobandAdapter.js} +0 -0
@@ -1,32 +1,93 @@
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 { registerStopTokenBroadcaster } from '../util/stopToken.js';
4
+ import BaseRpcDriver, { CORE_FREE_RESOURCES } from './BaseRpcDriver.js';
5
+ import RpcClient from './RpcClient.js';
6
+ import { deserializeError } from './serializeError/index.js';
7
+ function detectHardwareConcurrency() {
8
+ // fall back to 1 if navigator.hardwareConcurrency is absent, else clamp()
9
+ // sees NaN and collapses the pool to zero workers
10
+ return typeof navigator === 'undefined'
11
+ ? 1
12
+ : navigator.hardwareConcurrency || 1;
13
+ }
4
14
  class WebWorkerHandle {
5
15
  worker;
6
16
  client;
17
+ // a counter, not a nanoid: the listener map a channel keys into is this
18
+ // handle's own client, so that is the only scope uniqueness is needed in, and
19
+ // the nanoid was a crypto.getRandomValues per reporting call
20
+ channelCount = 0;
7
21
  constructor(worker) {
8
22
  this.worker = worker;
9
23
  this.client = new RpcClient(worker);
24
+ // Listen for worker errors that might not be caught by RpcClient
10
25
  this.client.on('error', error => {
11
26
  console.error('[WebWorker RPC Error]', error);
12
27
  });
13
28
  }
14
29
  destroy() {
30
+ // reject in-flight calls before terminating, else they wait on a reply the
31
+ // dead worker can never send
32
+ this.client.destroy();
15
33
  this.worker.terminate();
16
34
  }
17
- async call(funcName, args, opts) {
18
- const { statusCallback, rpcDriverClassName } = opts;
19
- const channel = `message-${nanoid()}`;
35
+ // lets the pool discard this handle once the worker throws a fatal error
36
+ onError(callback) {
37
+ this.client.on('error', callback);
38
+ }
39
+ notifyStopToken(id) {
40
+ this.client.notifyStopToken(id);
41
+ }
42
+ // the two halves of {@link WorkerHandle}'s plugin-facing pair
43
+ on(eventName, listener) {
44
+ this.client.on(eventName, listener);
45
+ }
46
+ postMessage(message) {
47
+ this.worker.postMessage(message);
48
+ }
49
+ /**
50
+ * A `channel` only when the caller asked for status, so that "no
51
+ * statusCallback" survives the worker boundary.
52
+ *
53
+ * It did not. The channel was minted unconditionally, and `wrapForRpc` builds
54
+ * the worker's `statusCallback` from whatever channel it is handed — so every
55
+ * method in every worker ran with a live status handle whoever called it had
56
+ * declined, and `MainThreadRpcDriver` (which passes the caller's own
57
+ * `undefined` straight through) answered the same question differently. That
58
+ * asymmetry is the one {@link RpcManager}'s `call` docstring already records
59
+ * in the other direction.
60
+ *
61
+ * The absence is not cosmetic — it is a documented branch. `downloadStatus`
62
+ * hands the reader no `onProgress` without a callback, `createProgressReporter`
63
+ * skips its emit, and every status the worker did send crossed a postMessage
64
+ * to reach a listener that dropped it.
65
+ *
66
+ * The postMessage traffic and the symmetry are the whole case; the read speed
67
+ * is not. `res.bytes()` is the SLOWER of the two reads under ~10MB —
68
+ * agent-docs/measurements/download-read-path.json — and an earlier revision of
69
+ * this comment claimed the opposite because four other places in the tree did.
70
+ */
71
+ async call(funcName, args,
72
+ // defaulted, not required: {@link WorkerHandle} declares it optional, and a
73
+ // `Core-extendWorker` wrapper written against that interface may well call
74
+ // `worker.call(name, args)` — which destructured `undefined` and threw
75
+ opts = {}) {
76
+ const { statusCallback } = opts;
77
+ if (!statusCallback) {
78
+ return this.client.call(funcName, args);
79
+ }
80
+ const channel = `message-${++this.channelCount}`;
81
+ // RpcClient is a generic event emitter (it also carries 'error' events), so
82
+ // its listeners see `unknown`. This channel is dedicated to one method's
83
+ // status emits, which the worker only ever posts as RpcStatus (see
84
+ // wrapForRpc in rpcWorker.ts), so narrowing to RpcStatus here is sound.
20
85
  const listener = (message) => {
21
- statusCallback?.(message);
86
+ statusCallback(message);
22
87
  };
23
88
  this.client.on(channel, listener);
24
89
  try {
25
- const result = await this.client.call(funcName, {
26
- ...args,
27
- channel,
28
- rpcDriverClassName,
29
- });
90
+ const result = await this.client.call(funcName, { ...args, channel });
30
91
  return result;
31
92
  }
32
93
  finally {
@@ -34,44 +95,268 @@ class WebWorkerHandle {
34
95
  }
35
96
  }
36
97
  }
98
+ class LazyWorker {
99
+ driver;
100
+ /**
101
+ * The handle this slot booted, and what the pool drives the worker's LIFE on
102
+ * — the error hook and the termination.
103
+ *
104
+ * Kept apart from {@link workerP} because a `Core-extendWorker` plugin only
105
+ * has to forward `call`: `WorkerHandle` makes `onError` and the rest
106
+ * optional, so a conforming wrapper (a spread plus a `call`, which is the
107
+ * obvious way to write one) drops them. Driving the re-boot through such a
108
+ * wrapper means a dead worker is never noticed and the slot never re-boots.
109
+ */
110
+ bootP;
111
+ /** What `Core-extendWorker` returned for it: where calls go. */
112
+ workerP;
113
+ constructor(driver) {
114
+ this.driver = driver;
115
+ }
116
+ async getWorker() {
117
+ if (!this.workerP) {
118
+ const booted = this.driver.makeWorker();
119
+ this.bootP = booted;
120
+ // once per booted worker by construction, rather than per dispatch behind
121
+ // a memo
122
+ this.workerP = booted.then(worker => this.driver.extendWorker(worker));
123
+ // drop this slot so the next getWorker re-boots, whether the boot failed
124
+ // or the booted worker later died (a dead worker never replies)
125
+ const invalidate = () => {
126
+ if (this.bootP === booted) {
127
+ this.bootP = undefined;
128
+ this.workerP = undefined;
129
+ }
130
+ };
131
+ booted
132
+ .then(worker => {
133
+ worker.onError?.(() => {
134
+ invalidate();
135
+ worker.destroy();
136
+ });
137
+ })
138
+ .catch(invalidate);
139
+ }
140
+ return this.workerP;
141
+ }
142
+ destroy() {
143
+ // terminate the underlying worker once it resolves; a worker that never
144
+ // booted (rejected promise) has nothing to terminate, so swallow that
145
+ this.bootP
146
+ ?.then(worker => {
147
+ worker.destroy();
148
+ })
149
+ .catch(() => { });
150
+ this.bootP = undefined;
151
+ this.workerP = undefined;
152
+ }
153
+ /**
154
+ * Forward a stopped token id, but never boot a worker to do it: an unbooted
155
+ * slot is running nothing to cancel. Routed through the same promise the
156
+ * dispatching call awaits, so a stop issued while this slot is still booting
157
+ * still lands after the call it means to cancel rather than ahead of the
158
+ * worker's message listener existing.
159
+ */
160
+ notifyStopToken(id) {
161
+ this.bootP
162
+ ?.then(worker => {
163
+ worker.notifyStopToken?.(id);
164
+ })
165
+ .catch(() => { });
166
+ }
167
+ /**
168
+ * Drop a session's cached adapters on this slot's worker — and, like
169
+ * {@link notifyStopToken}, never boot one to do it. A slot that never booted
170
+ * has no cache to free, and booting one there costs a whole worker bundle and
171
+ * every runtime plugin to say so.
172
+ *
173
+ * Through the extended handle, because it is a `call`: a plugin that wraps
174
+ * calls should see this one.
175
+ *
176
+ * Awaited rather than fire-and-forget, because a caller can be waiting to
177
+ * know the adapter is gone; a slot still booting frees once it lands.
178
+ */
179
+ async freeSession(sessionId) {
180
+ const worker = await this.workerP?.catch(() => undefined);
181
+ await worker?.call(CORE_FREE_RESOURCES, { sessionId });
182
+ }
183
+ }
184
+ /**
185
+ * Runs RPC methods in a pool of lazily-booted web workers, with our own
186
+ * state-group-aware round-robin assignment (one sticky worker per session) so a
187
+ * session's calls land on the same worker and can share cached adapters.
188
+ *
189
+ * The pool is here rather than in a `WorkerPoolRpcDriver` above it: that base
190
+ * abstracted `makeWorker`, which has one implementation. It is a plain
191
+ * overridable method now, which is all the seam was ever used for. ADR-086.
192
+ */
37
193
  export default class WebWorkerRpcDriver extends BaseRpcDriver {
38
- workerBootConfiguration;
194
+ options;
39
195
  name = 'WebWorkerRpcDriver';
40
- makeWorkerInstance;
41
- constructor(args, workerBootConfiguration) {
42
- super(args);
43
- this.workerBootConfiguration = workerBootConfiguration;
44
- this.makeWorkerInstance = args.makeWorkerInstance;
196
+ lastWorkerAssignment = -1;
197
+ // sessionId -> worker number
198
+ workerAssignments = new Map();
199
+ workerPool;
200
+ // a stopped token has to reach the thread actually running the work, and this
201
+ // is the seam that carries it. Broadcast rather than routed per call: one
202
+ // token is commonly in flight on several calls at once, and a worker holding
203
+ // nothing under that id ignores the frame.
204
+ //
205
+ // Registered with the POOL, not in the constructor, so that a driver which
206
+ // never boots a worker stays out of the module-global broadcaster set — and
207
+ // registered only once the pool exists to receive the broadcast, since a
208
+ // `createWorkerPool` that threw after registering left an entry no `destroy`
209
+ // could ever reach.
210
+ unregisterBroadcaster = () => { };
211
+ // `destroy` is terminal: `getWorkerPool` refuses rather than letting its `??=`
212
+ // build a second pool for a driver whose teardown already ran. ADR-086.
213
+ destroyed = false;
214
+ constructor(pluginManager, config, options) {
215
+ super(pluginManager, config);
216
+ this.options = options;
45
217
  }
218
+ /**
219
+ * Free the session on the worker it was assigned to, and drop the assignment
220
+ * so it doesn't accumulate for the life of the driver.
221
+ *
222
+ * A session with no assignment never dispatched anything, so there is nothing
223
+ * cached anywhere to free — and no pool to build in order to find that out.
224
+ */
225
+ async freeSession(sessionId) {
226
+ const workerNumber = this.workerAssignments.get(sessionId);
227
+ this.workerAssignments.delete(sessionId);
228
+ if (workerNumber !== undefined) {
229
+ await this.workerPool?.[workerNumber]?.freeSession(sessionId);
230
+ }
231
+ }
232
+ // terminate every pooled worker and reset assignment bookkeeping; call when
233
+ // discarding the driver so its worker threads don't outlive it
234
+ destroy() {
235
+ this.destroyed = true;
236
+ this.unregisterBroadcaster();
237
+ for (const worker of this.workerPool ?? []) {
238
+ worker.destroy();
239
+ }
240
+ this.workerPool = undefined;
241
+ this.workerAssignments.clear();
242
+ this.lastWorkerAssignment = -1;
243
+ }
244
+ createWorkerPool() {
245
+ // workerCount 0 (the config default) means "decide from hardware"
246
+ const workerCount = readConfObject(this.config, 'workerCount') ||
247
+ clamp(detectHardwareConcurrency() - 1, 1, 5);
248
+ const pool = Array.from({ length: workerCount }, () => new LazyWorker(this));
249
+ this.unregisterBroadcaster = registerStopTokenBroadcaster(id => {
250
+ for (const worker of pool) {
251
+ worker.notifyStopToken(id);
252
+ }
253
+ });
254
+ return pool;
255
+ }
256
+ getWorkerPool() {
257
+ if (this.destroyed) {
258
+ throw new Error(`${this.name} was destroyed`);
259
+ }
260
+ return (this.workerPool ??= this.createWorkerPool());
261
+ }
262
+ async getWorker(sessionId) {
263
+ const workers = this.getWorkerPool();
264
+ let workerNumber = this.workerAssignments.get(sessionId);
265
+ if (workerNumber === undefined) {
266
+ workerNumber = (this.lastWorkerAssignment + 1) % workers.length;
267
+ this.workerAssignments.set(sessionId, workerNumber);
268
+ this.lastWorkerAssignment = workerNumber;
269
+ }
270
+ return workers[workerNumber].getWorker();
271
+ }
272
+ /**
273
+ * Hand a freshly booted worker to whatever plugins want to extend it, and use
274
+ * whatever comes back as the pooled handle.
275
+ *
276
+ * Called from {@link LazyWorker.getWorker} rather than from `makeWorker`,
277
+ * which subclasses override — a seam that skipped the fold would silently
278
+ * un-extend every worker. It answers "what is this worker", not "what is this
279
+ * call", so folding at dispatch needed a WeakMap to stop rebuilding a
280
+ * plugin's wrapper per RPC; once per boot has nothing to memoize.
281
+ */
282
+ extendWorker(worker) {
283
+ return this.pluginManager.evaluateExtensionPoint(
284
+ /** #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 */
285
+ 'Core-extendWorker', worker);
286
+ }
287
+ // get this session's sticky worker and hand off the already-serialized args
288
+ async transport(sessionId, rpcMethod, serializedArgs, statusCallback) {
289
+ const worker = await this.getWorker(sessionId);
290
+ return worker.call(rpcMethod.name, serializedArgs, { statusCallback });
291
+ }
292
+ /**
293
+ * Boot one worker and run the configuration handshake. Overridable so a test
294
+ * can hand the pool a fake handle without a `Worker`; nothing in the app does.
295
+ */
46
296
  async makeWorker() {
47
- const instance = this.makeWorkerInstance();
297
+ // one RpcClient per worker so we can do our own state-group-aware load
298
+ // balancing across the pool
299
+ const instance = this.options.makeWorkerInstance();
48
300
  const handle = new WebWorkerHandle(instance);
49
301
  const isSafari = /^((?!chrome|android).)*safari/i.test(navigator.userAgent);
50
302
  if (isSafari) {
303
+ // xref https://github.com/GMOD/jbrowse-components/issues/3245
304
+ // eslint-disable-next-line no-console
51
305
  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
306
  }
307
+ // send the worker its boot configuration using info from the pluginManager
53
308
  return new Promise((resolve, reject) => {
54
- const listener = (e) => {
309
+ const cleanup = () => {
310
+ instance.removeEventListener('message', onMessage);
311
+ instance.removeEventListener('error', onError);
312
+ };
313
+ // the pool discards this slot and re-boots on the next call, so terminate
314
+ // the half-booted worker rather than orphaning its thread
315
+ const fail = (error) => {
316
+ cleanup();
317
+ handle.destroy();
318
+ reject(error);
319
+ };
320
+ const onMessage = (e) => {
55
321
  switch (e.data.message) {
56
322
  case 'ready': {
323
+ cleanup();
57
324
  resolve(handle);
58
- instance.removeEventListener('message', listener);
59
325
  break;
60
326
  }
61
327
  case 'readyForConfig': {
62
- instance.postMessage({
63
- message: 'config',
64
- config: this.workerBootConfiguration,
65
- });
328
+ // The worker is waiting in receiveConfiguration(), which has no
329
+ // timeout, and this listener's throw would escape before cleanup or
330
+ // fail could run — so an unclonable boot configuration left both
331
+ // sides waiting forever rather than reporting anything.
332
+ try {
333
+ const { plugins, windowHref, numberGrouping } = this.options;
334
+ instance.postMessage({
335
+ message: 'config',
336
+ config: { plugins, windowHref, numberGrouping },
337
+ });
338
+ }
339
+ catch (e) {
340
+ fail(new Error(`could not send the worker its boot configuration`, {
341
+ cause: e,
342
+ }));
343
+ }
66
344
  break;
67
345
  }
68
346
  case 'error': {
69
- reject(deserializeError(e.data.error));
347
+ fail(deserializeError(e.data.error));
70
348
  break;
71
349
  }
350
+ // No default
72
351
  }
73
352
  };
74
- instance.addEventListener('message', listener);
353
+ // a worker that throws while loading its script posts no message, so
354
+ // reject on the raw ErrorEvent too, else the boot promise hangs forever
355
+ const onError = (e) => {
356
+ fail(new Error(e.message || 'worker failed to load'));
357
+ };
358
+ instance.addEventListener('message', onMessage);
359
+ instance.addEventListener('error', onError);
75
360
  });
76
361
  }
77
362
  }
@@ -0,0 +1,58 @@
1
+ import type { StatusCallback } from '../util/progress.ts';
2
+ import type { StopToken, StopTokenChecker } from '../util/stopToken.ts';
3
+ import type { AugmentedRegion } from '../util/types/data.ts';
4
+ /**
5
+ * Which question a byte budget asks of a region set: the gate's per-region
6
+ * budget, or the save dialog's bound on the whole download.
7
+ */
8
+ export type ByteEstimateScope = 'largestRegion' | 'wholeRequest';
9
+ /**
10
+ * The one spelling of a gated feature RPC's budget argument: the number the
11
+ * worker measures against, undefined when the gate declined to act and nothing
12
+ * is measured. A call-site argument, never part of `rpcProps`, because it
13
+ * swings at 20kb and on force-load.
14
+ */
15
+ export interface GatedFetchArgs {
16
+ byteLimit?: number;
17
+ }
18
+ export interface ByteMeasurableAdapter {
19
+ getRegionByteSize: (regions: AugmentedRegion[], opts?: {
20
+ stopToken?: StopToken;
21
+ statusCallback?: StatusCallback;
22
+ }) => Promise<number | undefined>;
23
+ }
24
+ /**
25
+ * What a gated fetch RPC answers instead of a payload when a region is over
26
+ * budget on either axis, carrying everything measured on the way: the byte
27
+ * stage runs first, so a density refusal still has `bytes`.
28
+ */
29
+ export interface RegionTooLargeResult {
30
+ regionTooLarge: true;
31
+ featureCount?: number;
32
+ bytes?: number;
33
+ }
34
+ export declare function isRegionRefused(result: unknown): result is RegionTooLargeResult;
35
+ /** Undefined, never 0, when no region could be measured. */
36
+ export declare function largestRegionBytes(perRegion: (number | undefined)[]): number | undefined;
37
+ /** A non-positive declared limit means "no opinion" (htsget reports 0). */
38
+ export declare function adapterByteLimit(declared: unknown, fallback: number): number;
39
+ export declare function overByteBudget(bytes: number | undefined, byteLimit: number | undefined): bytes is number;
40
+ /** The bytes a fetch result reports, payload or refusal; absent means unmeasured. */
41
+ export declare function measuredBytes(result: unknown): number | undefined;
42
+ /**
43
+ * The first await of every gated feature fetch: each region's index-only byte
44
+ * estimate, judged by the largest because the budget is per region. `bytes`
45
+ * comes back either way; when `tooLarge` is set the caller returns it and
46
+ * fetches nothing. No budget means no measurement.
47
+ */
48
+ export declare function measureRegionBytes({ dataAdapter, regions, byteLimit, stopToken, statusCallback, stopTokenCheck, }: {
49
+ dataAdapter: ByteMeasurableAdapter;
50
+ regions: AugmentedRegion[];
51
+ byteLimit: number | undefined;
52
+ stopToken?: StopToken;
53
+ statusCallback?: StatusCallback;
54
+ stopTokenCheck?: StopTokenChecker;
55
+ }): Promise<{
56
+ bytes?: number;
57
+ tooLarge?: RegionTooLargeResult;
58
+ }>;
@@ -0,0 +1,50 @@
1
+ import { updateStatus } from '../util/progress.js';
2
+ import { checkStopTokenThrottled } from '../util/stopToken.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
+ * The first await of every gated feature fetch: each region's index-only byte
34
+ * estimate, judged by the largest because the budget is per region. `bytes`
35
+ * comes back either way; when `tooLarge` is set the caller returns it and
36
+ * fetches nothing. No budget means no measurement.
37
+ */
38
+ export async function measureRegionBytes({ dataAdapter, regions, byteLimit, stopToken, statusCallback, stopTokenCheck, }) {
39
+ if (byteLimit === undefined) {
40
+ return {};
41
+ }
42
+ const bytes = largestRegionBytes(await updateStatus('Checking region size', statusCallback, () => Promise.all(regions.map(region => dataAdapter.getRegionByteSize([region], {
43
+ stopToken,
44
+ statusCallback,
45
+ })))));
46
+ checkStopTokenThrottled(stopTokenCheck);
47
+ return overByteBudget(bytes, byteLimit)
48
+ ? { bytes, tooLarge: { regionTooLarge: true, bytes } }
49
+ : { bytes };
50
+ }
@@ -1,9 +1,31 @@
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;
5
- defaultValue: string;
6
+ /**
7
+ * #slot
8
+ * which RPC backend to use. Empty means "use the host application's
9
+ * default" (web/desktop default to the web worker driver, embedded/headless
10
+ * to the main thread). Every call in the session runs on the driver this
11
+ * names; there is no per-track or per-call override.
12
+ */
13
+ readonly defaultDriver: {
14
+ readonly type: "string";
15
+ readonly description: "the RPC driver to run data fetching on: MainThreadRpcDriver or WebWorkerRpcDriver. Leave empty to use the default for this application";
16
+ readonly defaultValue: "";
17
+ readonly advanced: true;
18
+ };
19
+ /**
20
+ * #slot
21
+ * number of web workers to spawn for the web worker RPC driver. 0 lets
22
+ * JBrowse pick based on hardware concurrency.
23
+ */
24
+ readonly workerCount: {
25
+ readonly type: "number";
26
+ readonly description: "The number of workers to use. If 0 (the default) JBrowse will decide how many workers to use.";
27
+ readonly defaultValue: 0;
28
+ readonly advanced: true;
6
29
  };
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
30
  }, import("../configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
9
31
  export default _default;
@@ -1,22 +1,46 @@
1
- import { types } from '@jbrowse/mobx-state-tree';
2
- import MainThreadRpcDriverConfigSchema from "./mainThreadRpcConfig.js";
3
- import WebWorkerRpcDriverConfigSchema from "./webWorkerRpcConfig.js";
4
- import { ConfigurationSchema } from "../configuration/index.js";
5
- function x() { }
1
+ import { ConfigurationSchema } from '../configuration/index.js';
2
+ /**
3
+ * #config RpcOptions
4
+ * #category root
5
+ */
6
6
  export default ConfigurationSchema('RpcOptions', {
7
+ /**
8
+ * #slot
9
+ * which RPC backend to use. Empty means "use the host application's
10
+ * default" (web/desktop default to the web worker driver, embedded/headless
11
+ * to the main thread). Every call in the session runs on the driver this
12
+ * names; there is no per-track or per-call override.
13
+ */
7
14
  defaultDriver: {
8
15
  type: 'string',
9
- description: 'the RPC driver to use for tracks and tasks that are not configured to use a specific RPC backend',
10
- defaultValue: 'MainThreadRpcDriver',
16
+ description: 'the RPC driver to run data fetching on: MainThreadRpcDriver or WebWorkerRpcDriver. Leave empty to use the default for this application',
17
+ defaultValue: '',
18
+ advanced: true,
19
+ },
20
+ /**
21
+ * #slot
22
+ * number of web workers to spawn for the web worker RPC driver. 0 lets
23
+ * JBrowse pick based on hardware concurrency.
24
+ */
25
+ workerCount: {
26
+ type: 'number',
27
+ description: 'The number of workers to use. If 0 (the default) JBrowse will decide how many workers to use.',
28
+ defaultValue: 0,
29
+ advanced: true,
11
30
  },
12
- drivers: types.optional(types.map(types.union(MainThreadRpcDriverConfigSchema, WebWorkerRpcDriverConfigSchema)), {
13
- MainThreadRpcDriver: { type: 'MainThreadRpcDriver' },
14
- WebWorkerRpcDriver: { type: 'WebWorkerRpcDriver' },
15
- }),
16
31
  }, {
17
- actions: (self) => ({
18
- addDriverConfig(configName, configSnapshot) {
19
- self.drivers.set(configName, configSnapshot);
20
- },
21
- }),
32
+ // legacy sessions stored per-driver config under a `drivers` map
33
+ // (`{ WebWorkerRpcDriver: { workerCount } }`); hoist any saved workerCount
34
+ // to the flat slot and drop the map so the snapshot validates.
35
+ preProcessSnapshot(snapshot) {
36
+ if ('drivers' in snapshot) {
37
+ const { drivers, ...rest } = snapshot;
38
+ const legacyWorkerCount = drivers?.WebWorkerRpcDriver?.workerCount ??
39
+ drivers?.MainThreadRpcDriver?.workerCount;
40
+ return rest.workerCount === undefined && legacyWorkerCount !== undefined
41
+ ? { ...rest, workerCount: legacyWorkerCount }
42
+ : rest;
43
+ }
44
+ return snapshot;
45
+ },
22
46
  });
@@ -1,12 +1,10 @@
1
1
  export { default as CoreGetRefNames } from './methods/CoreGetRefNames.ts';
2
- export { default as CoreGetFeatureDetails } from './methods/CoreGetFeatureDetails.ts';
3
2
  export { default as CoreGetMetadata } from './methods/CoreGetMetadata.ts';
4
- export { default as CoreGetFileInfo } from './methods/CoreGetFileInfo.ts';
3
+ export { default as CoreGetInfo } from './methods/CoreGetInfo.ts';
5
4
  export { default as CoreGetFeatures } from './methods/CoreGetFeatures.ts';
6
5
  export { default as CoreGetSequence } from './methods/CoreGetSequence.ts';
7
- export { default as CoreRender } from './methods/CoreRender.ts';
8
6
  export { default as CoreFreeResources } from './methods/CoreFreeResources.ts';
9
- export { default as CoreGetFeatureDensityStats } from './methods/CoreGetFeatureDensityStats.ts';
7
+ export { default as CoreGetRegionByteEstimate } from './methods/CoreGetRegionByteEstimate.ts';
8
+ export { default as CoreGetFeatureDensity } from './methods/CoreGetFeatureDensity.ts';
10
9
  export { default as CoreGetRegions } from './methods/CoreGetRegions.ts';
11
10
  export { default as CoreGetExportData } from './methods/CoreGetExportData.ts';
12
- export { type RenderArgs } from './methods/util.ts';
@@ -1,12 +1,10 @@
1
- export { default as CoreGetRefNames } from "./methods/CoreGetRefNames.js";
2
- export { default as CoreGetFeatureDetails } from "./methods/CoreGetFeatureDetails.js";
3
- export { default as CoreGetMetadata } from "./methods/CoreGetMetadata.js";
4
- export { default as CoreGetFileInfo } from "./methods/CoreGetFileInfo.js";
5
- export { default as CoreGetFeatures } from "./methods/CoreGetFeatures.js";
6
- export { default as CoreGetSequence } from "./methods/CoreGetSequence.js";
7
- export { default as CoreRender } from "./methods/CoreRender.js";
8
- export { default as CoreFreeResources } from "./methods/CoreFreeResources.js";
9
- export { default as CoreGetFeatureDensityStats } from "./methods/CoreGetFeatureDensityStats.js";
10
- export { default as CoreGetRegions } from "./methods/CoreGetRegions.js";
11
- export { default as CoreGetExportData } from "./methods/CoreGetExportData.js";
12
- export {} from "./methods/util.js";
1
+ export { default as CoreGetRefNames } from './methods/CoreGetRefNames.js';
2
+ export { default as CoreGetMetadata } from './methods/CoreGetMetadata.js';
3
+ export { default as CoreGetInfo } from './methods/CoreGetInfo.js';
4
+ export { default as CoreGetFeatures } from './methods/CoreGetFeatures.js';
5
+ export { default as CoreGetSequence } from './methods/CoreGetSequence.js';
6
+ export { default as CoreFreeResources } from './methods/CoreFreeResources.js';
7
+ export { default as CoreGetRegionByteEstimate } from './methods/CoreGetRegionByteEstimate.js';
8
+ export { default as CoreGetFeatureDensity } from './methods/CoreGetFeatureDensity.js';
9
+ export { default as CoreGetRegions } from './methods/CoreGetRegions.js';
10
+ export { default as CoreGetExportData } from './methods/CoreGetExportData.js';