@jbrowse/core 4.3.0 → 5.0.0-beta.1

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 (1124) hide show
  1. package/README.md +783 -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 +40 -40
  113. package/esm/PluginLoader.js +166 -82
  114. package/esm/PluginManager.d.ts +368 -55
  115. package/esm/PluginManager.js +326 -85
  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 +84 -65
  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/TextSearch/BaseResults.d.ts +20 -21
  135. package/esm/TextSearch/BaseResults.js +8 -33
  136. package/esm/TextSearch/TextSearchManager.d.ts +14 -34
  137. package/esm/TextSearch/TextSearchManager.js +87 -34
  138. package/esm/assemblyManager/assembly.d.ts +307 -34
  139. package/esm/assemblyManager/assembly.js +551 -262
  140. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  141. package/esm/assemblyManager/assemblyAdapters.js +18 -0
  142. package/esm/assemblyManager/assemblyConfigSchema.d.ts +192 -17
  143. package/esm/assemblyManager/assemblyConfigSchema.js +213 -19
  144. package/esm/assemblyManager/assemblyManager.d.ts +711 -303
  145. package/esm/assemblyManager/assemblyManager.js +351 -46
  146. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +32 -0
  147. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +85 -0
  148. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  149. package/esm/assemblyManager/geneticCodes.js +47 -0
  150. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +9 -0
  151. package/esm/assemblyManager/getSequenceAdapterConfig.js +12 -0
  152. package/esm/assemblyManager/index.d.ts +1 -1
  153. package/esm/assemblyManager/index.js +2 -2
  154. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  155. package/esm/assemblyManager/loadRefNameMap.js +80 -0
  156. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  157. package/esm/assemblyManager/refNameColors.js +32 -0
  158. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  159. package/esm/assemblyManager/refNameMaps.js +87 -0
  160. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  161. package/esm/assemblyManager/refNameMismatch.js +66 -0
  162. package/esm/checkPlugins.d.ts +11 -0
  163. package/esm/checkPlugins.js +77 -0
  164. package/esm/configuration/configurationSchema.d.ts +154 -19
  165. package/esm/configuration/configurationSchema.js +359 -138
  166. package/esm/configuration/configurationSlot.d.ts +283 -30
  167. package/esm/configuration/configurationSlot.js +205 -226
  168. package/esm/configuration/formatAboutConfigSchema.d.ts +55 -0
  169. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  170. package/esm/configuration/formatDetailsConfigSchema.d.ts +80 -0
  171. package/esm/configuration/formatDetailsConfigSchema.js +90 -0
  172. package/esm/configuration/fullConfSnapshot.d.ts +28 -0
  173. package/esm/configuration/fullConfSnapshot.js +66 -0
  174. package/esm/configuration/getConf.d.ts +88 -0
  175. package/esm/configuration/getConf.js +74 -0
  176. package/esm/configuration/index.d.ts +19 -3
  177. package/esm/configuration/index.js +19 -2
  178. package/esm/configuration/mergeFormatCallbacks.d.ts +15 -0
  179. package/esm/configuration/mergeFormatCallbacks.js +24 -0
  180. package/esm/configuration/promotableDefaults.d.ts +199 -0
  181. package/esm/configuration/promotableDefaults.js +326 -0
  182. package/esm/configuration/promotablePin.d.ts +55 -0
  183. package/esm/configuration/promotableResolve.d.ts +108 -0
  184. package/esm/configuration/promotableResolve.js +117 -0
  185. package/esm/configuration/promotableSlots.d.ts +12 -0
  186. package/esm/configuration/promotableSlots.js +45 -0
  187. package/esm/configuration/readConfObject.d.ts +56 -0
  188. package/esm/configuration/readConfObject.js +161 -0
  189. package/esm/configuration/schemaRegistry.d.ts +35 -0
  190. package/esm/configuration/schemaRegistry.js +50 -0
  191. package/esm/configuration/schemaTypes.d.ts +23 -0
  192. package/esm/configuration/schemaTypes.js +94 -0
  193. package/esm/configuration/slotFacade.d.ts +82 -0
  194. package/esm/configuration/slotFacade.js +89 -0
  195. package/esm/configuration/slotShape.d.ts +12 -0
  196. package/esm/configuration/slotShape.js +84 -0
  197. package/esm/configuration/slotValueUtils.d.ts +17 -0
  198. package/esm/configuration/slotValueUtils.js +25 -0
  199. package/esm/configuration/tabixIndexFields.d.ts +44 -0
  200. package/esm/configuration/tabixIndexFields.js +45 -0
  201. package/esm/configuration/tabixShorthand.d.ts +34 -0
  202. package/esm/configuration/tabixShorthand.js +45 -0
  203. package/esm/configuration/types.d.ts +170 -7
  204. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +24 -10
  205. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +23 -15
  206. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +120 -7
  207. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +99 -27
  208. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  209. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  210. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  211. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  212. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  213. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  214. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  215. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  216. package/esm/data_adapters/BaseAdapter/index.d.ts +6 -4
  217. package/esm/data_adapters/BaseAdapter/index.js +5 -5
  218. package/esm/data_adapters/BaseAdapter/stats.d.ts +5 -5
  219. package/esm/data_adapters/BaseAdapter/stats.js +48 -22
  220. package/esm/data_adapters/BaseAdapter/types.d.ts +10 -8
  221. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  222. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  223. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  224. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  225. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +4 -4
  226. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +36 -4
  227. package/esm/data_adapters/CytobandAdapter/configSchema.js +46 -2
  228. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  229. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  230. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  231. package/esm/data_adapters/dataAdapterCache.d.ts +35 -1
  232. package/esm/data_adapters/dataAdapterCache.js +62 -22
  233. package/esm/data_adapters/getFeatureAdapter.d.ts +22 -0
  234. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  235. package/esm/data_adapters/getSequenceSubAdapter.d.ts +21 -0
  236. package/esm/data_adapters/getSequenceSubAdapter.js +44 -0
  237. package/esm/pluggableElementTypes/AdapterType.d.ts +52 -2
  238. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  239. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  240. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  241. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  242. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  243. package/esm/pluggableElementTypes/DisplayType.d.ts +10 -0
  244. package/esm/pluggableElementTypes/DisplayType.js +14 -1
  245. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  246. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +13 -0
  247. package/esm/pluggableElementTypes/PluggableElementBase.js +13 -0
  248. package/esm/pluggableElementTypes/RpcMethodType.d.ts +132 -12
  249. package/esm/pluggableElementTypes/RpcMethodType.js +263 -98
  250. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +19 -9
  251. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  252. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  253. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  254. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  255. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  256. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +3 -3
  257. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  258. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  259. package/esm/pluggableElementTypes/TrackType.js +1 -1
  260. package/esm/pluggableElementTypes/ViewType.d.ts +2 -1
  261. package/esm/pluggableElementTypes/ViewType.js +9 -2
  262. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  263. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  264. package/esm/pluggableElementTypes/addMenuItems.d.ts +87 -0
  265. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  266. package/esm/pluggableElementTypes/extendElementType.d.ts +30 -0
  267. package/esm/pluggableElementTypes/extendElementType.js +68 -0
  268. package/esm/pluggableElementTypes/index.d.ts +7 -7
  269. package/esm/pluggableElementTypes/index.js +24 -14
  270. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +70 -15
  271. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  272. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +605 -84
  273. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +172 -64
  274. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +195 -35
  275. package/esm/pluggableElementTypes/models/BaseTrackModel.js +332 -85
  276. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +167 -16
  277. package/esm/pluggableElementTypes/models/BaseViewModel.js +111 -16
  278. package/esm/pluggableElementTypes/models/HighlightsMixin.d.ts +51 -0
  279. package/esm/pluggableElementTypes/models/HighlightsMixin.js +78 -0
  280. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +163 -29
  281. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  282. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +174 -0
  283. package/esm/pluggableElementTypes/models/assertDisplayContract.js +246 -0
  284. package/esm/pluggableElementTypes/models/baseConnectionConfig.d.ts +22 -8
  285. package/esm/pluggableElementTypes/models/baseConnectionConfig.js +18 -2
  286. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +39 -20
  287. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.js +23 -2
  288. package/esm/pluggableElementTypes/models/baseTrackConfig.d.ts +181 -65
  289. package/esm/pluggableElementTypes/models/baseTrackConfig.js +191 -89
  290. package/esm/pluggableElementTypes/models/components/SaveTrackData.d.ts +3 -8
  291. package/esm/pluggableElementTypes/models/components/SaveTrackData.js +113 -139
  292. package/esm/pluggableElementTypes/models/components/fetchTrackData.d.ts +55 -0
  293. package/esm/pluggableElementTypes/models/components/fetchTrackData.js +83 -0
  294. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.d.ts +40 -0
  295. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.js +115 -0
  296. package/esm/pluggableElementTypes/models/index.d.ts +6 -3
  297. package/esm/pluggableElementTypes/models/index.js +10 -8
  298. package/esm/pluggableElementTypes/models/migrateTrackConfig.d.ts +34 -0
  299. package/esm/pluggableElementTypes/models/migrateTrackConfig.js +54 -0
  300. package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.js +75 -7
  301. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.d.ts +9 -3
  302. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +153 -103
  303. package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.d.ts +6 -1
  304. package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.js +70 -74
  305. package/esm/pluggableElementTypes/models/saveTrackFileTypes/types.d.ts +9 -1
  306. package/esm/pluggableElementTypes/models/saveTrackFileTypes/util.d.ts +21 -0
  307. package/esm/pluggableElementTypes/models/saveTrackFileTypes/util.js +51 -0
  308. package/esm/pluggableElementTypes/models/uriMatchesDomains.d.ts +29 -0
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  1024. package/esm/util/viewStatus.d.ts +58 -0
  1025. package/esm/util/viewStatus.js +20 -0
  1026. package/esm/util/virtualRange.d.ts +36 -0
  1027. package/esm/util/virtualRange.js +26 -0
  1028. package/esm/util/webStorage.d.ts +26 -0
  1029. package/esm/util/webStorage.js +92 -0
  1030. package/esm/util/wheelZoom.d.ts +59 -0
  1031. package/esm/util/wheelZoom.js +231 -0
  1032. package/esm/util/whenViewSettled.d.ts +27 -0
  1033. package/esm/util/whenViewSettled.js +28 -0
  1034. package/esm/util/withFeatureDetails.d.ts +34 -0
  1035. package/esm/util/withFeatureDetails.js +59 -0
  1036. package/package.json +240 -820
  1037. package/esm/ReExports/DataGrid.d.ts +0 -1
  1038. package/esm/ReExports/DataGrid.js +0 -1
  1039. package/esm/configuration/util.d.ts +0 -10
  1040. package/esm/configuration/util.js +0 -123
  1041. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
  1042. package/esm/data_adapters/util.d.ts +0 -1
  1043. package/esm/data_adapters/util.js +0 -6
  1044. package/esm/pluggableElementTypes/GlyphType.d.ts +0 -43
  1045. package/esm/pluggableElementTypes/GlyphType.js +0 -18
  1046. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +0 -5
  1047. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +0 -17
  1048. package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +0 -52
  1049. package/esm/pluggableElementTypes/renderers/BoxRendererType.js +0 -78
  1050. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +0 -4
  1051. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +0 -4
  1052. package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -58
  1053. package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +0 -77
  1054. package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +0 -31
  1055. package/esm/pluggableElementTypes/renderers/LayoutSession.js +0 -40
  1056. package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
  1057. package/esm/pluggableElementTypes/renderers/RendererType.js +0 -20
  1058. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +0 -58
  1059. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.js +0 -108
  1060. package/esm/pluggableElementTypes/renderers/index.d.ts +0 -6
  1061. package/esm/pluggableElementTypes/renderers/index.js +0 -6
  1062. package/esm/pluggableElementTypes/renderers/util.d.ts +0 -3
  1063. package/esm/pluggableElementTypes/renderers/util.js +0 -14
  1064. package/esm/rpc/baseRpcConfig.d.ts +0 -8
  1065. package/esm/rpc/baseRpcConfig.js +0 -10
  1066. package/esm/rpc/mainThreadRpcConfig.d.ts +0 -8
  1067. package/esm/rpc/mainThreadRpcConfig.js +0 -8
  1068. package/esm/rpc/methods/CoreGetFeatureDensityStats.d.ts +0 -17
  1069. package/esm/rpc/methods/CoreGetFeatureDensityStats.js +0 -25
  1070. package/esm/rpc/methods/CoreGetFeatureDetails.d.ts +0 -11
  1071. package/esm/rpc/methods/CoreGetFeatureDetails.js +0 -24
  1072. package/esm/rpc/methods/CoreGetFileInfo.d.ts +0 -9
  1073. package/esm/rpc/methods/CoreGetFileInfo.js +0 -15
  1074. package/esm/rpc/methods/CoreRender.d.ts +0 -14
  1075. package/esm/rpc/methods/CoreRender.js +0 -40
  1076. package/esm/rpc/methods/CoreSaveFeatureData.d.ts +0 -16
  1077. package/esm/rpc/methods/CoreSaveFeatureData.js +0 -32
  1078. package/esm/rpc/methods/util.d.ts +0 -15
  1079. package/esm/rpc/methods/util.js +0 -7
  1080. package/esm/rpc/webWorkerRpcConfig.d.ts +0 -8
  1081. package/esm/rpc/webWorkerRpcConfig.js +0 -8
  1082. package/esm/ui/MenuButton.d.ts +0 -1
  1083. package/esm/ui/MenuButton.js +0 -1
  1084. package/esm/ui/MenuItems.d.ts +0 -15
  1085. package/esm/ui/MenuItems.js +0 -59
  1086. package/esm/ui/useEvent.d.ts +0 -1
  1087. package/esm/ui/useEvent.js +0 -10
  1088. package/esm/util/blobToDataURL.d.ts +0 -1
  1089. package/esm/util/blobToDataURL.js +0 -14
  1090. package/esm/util/compositeMap.d.ts +0 -11
  1091. package/esm/util/compositeMap.js +0 -59
  1092. package/esm/util/flatqueue/index.d.ts +0 -11
  1093. package/esm/util/flatqueue/index.js +0 -61
  1094. package/esm/util/layouts/BaseLayout.d.ts +0 -30
  1095. package/esm/util/layouts/MultiLayout.d.ts +0 -12
  1096. package/esm/util/layouts/MultiLayout.js +0 -40
  1097. package/esm/util/layouts/PileupLayout.d.ts +0 -41
  1098. package/esm/util/layouts/PileupLayout.js +0 -202
  1099. package/esm/util/layouts/PrecomputedLayout.d.ts +0 -30
  1100. package/esm/util/layouts/PrecomputedLayout.js +0 -71
  1101. package/esm/util/layouts/SceneGraph.d.ts +0 -31
  1102. package/esm/util/layouts/SceneGraph.js +0 -121
  1103. package/esm/util/makeAbortableReaction.d.ts +0 -3
  1104. package/esm/util/makeAbortableReaction.js +0 -47
  1105. package/esm/util/map-obj/index.d.ts +0 -13
  1106. package/esm/util/map-obj/index.js +0 -92
  1107. package/esm/util/nextTick.d.ts +0 -1
  1108. package/esm/util/nextTick.js +0 -3
  1109. package/esm/util/offscreenCanvasGetSerializingSvg.d.ts +0 -5
  1110. package/esm/util/offscreenCanvasGetSerializingSvg.js +0 -9
  1111. package/esm/util/offscreenCanvasUtils.d.ts +0 -12
  1112. package/esm/util/offscreenCanvasUtils.js +0 -19
  1113. package/esm/util/renderToAbstractCanvas.d.ts +0 -17
  1114. package/esm/util/renderToAbstractCanvas.js +0 -53
  1115. package/esm/util/transferables.d.ts +0 -2
  1116. package/esm/util/transferables.js +0 -35
  1117. package/esm/util/tss-react/mui/index.d.ts +0 -1
  1118. package/esm/util/tss-react/mui/index.js +0 -1
  1119. package/esm/util/tss-react/mui/mui.d.ts +0 -10
  1120. package/esm/util/tss-react/mui/mui.js +0 -5
  1121. package/esm/util/when.d.ts +0 -1
  1122. package/esm/util/when.js +0 -1
  1123. /package/esm/{data_adapters/BaseAdapter/BaseOptions.js → configuration/promotablePin.js} +0 -0
  1124. /package/esm/{util/layouts/BaseLayout.js → data_adapters/BaseAdapter/CytobandAdapter.js} +0 -0
@@ -0,0 +1,220 @@
1
+ /**
2
+ * What a plugin definition is, and everything that can be answered by looking
3
+ * at one — its url, its name, whether two describe the same plugin.
4
+ *
5
+ * Kept apart from PluginLoader, which pulls in ReExports (effectively all of
6
+ * core) to be able to run a plugin. Inspecting a definition must not cost that:
7
+ * the plugin store resolves definitions and would otherwise import core's
8
+ * config layer back into itself.
9
+ */
10
+ export function isUMDPluginDefinition(def) {
11
+ return 'umdUrl' in def || 'url' in def || 'umdLoc' in def;
12
+ }
13
+ export function isESMPluginDefinition(def) {
14
+ return 'esmUrl' in def || 'esmLoc' in def;
15
+ }
16
+ export function isCJSPluginDefinition(def) {
17
+ return 'cjsUrl' in def;
18
+ }
19
+ /**
20
+ * Whether a definition names a store entry to resolve. Deliberately not part of
21
+ * the CJS/ESM/UMD trio `assertSingleKind` counts: those are loaders, and a ref
22
+ * is not one. A ref names *which plugin*, and pairing it with a url is the
23
+ * supported migration shape rather than the two-loaders ambiguity that guard
24
+ * exists to refuse.
25
+ */
26
+ export function isStorePluginDefinition(def) {
27
+ return 'storePlugin' in def && typeof def.storePlugin === 'string';
28
+ }
29
+ /** The store entry a definition names, resolved or not. */
30
+ export function storePluginName(def) {
31
+ return isStorePluginDefinition(def) ? def.storePlugin : undefined;
32
+ }
33
+ // Plugins that used to ship as external config `plugins[]` entries but are now
34
+ // bundled into the jbrowse-web/desktop core build. Remote configs on jbrowse.org
35
+ // still list them, so we drop those entries before loading: core already
36
+ // registers the same elements (and wins, since core plugins register first), and
37
+ // skipping the external copy avoids a redundant network fetch plus a flurry of
38
+ // "already registered" console warnings. Matched on the config-level `name`
39
+ // (the external plugin's UMD-global name, e.g. "MafViewer"/"GWAS"), not the core
40
+ // class name — so this runs AFTER `resolveStorePluginRefs`, which is where a
41
+ // store ref acquires the name to match on. Run it before, and a config naming a
42
+ // vendored plugin by package slips through and installs a second copy beside
43
+ // core's. Apply only in products whose core bundle actually vendors these —
44
+ // not globally — so CLI indexing, @jbrowse/img, and react-circular (which don't
45
+ // bundle them) still load the external plugin. Also drives the plugin store,
46
+ // which hides these so a user can't install a colliding second copy
47
+ // (`installablePlugins`, util/pluginStore.ts).
48
+ export const vendoredPluginNames = new Set(['MafViewer', 'GWAS']);
49
+ /**
50
+ * Desktop's half of the same list — a plugin one product bundles and another does
51
+ * not, which the shared set above cannot express.
52
+ *
53
+ * Blat is in Desktop's corePlugins but deliberately not Web's: Web is where
54
+ * cold-load bundle size is paid, and BLAT is niche. So Desktop's bundled copy is
55
+ * the only one that ships. It is what gives BLAT on a genome the user opened
56
+ * from their own disk, where no config names any plugin, and it is the copy that
57
+ * reaches UCSC through the main-process `blatFetch` bridge and the CAPTCHA-solve
58
+ * window. Web has to load the external entry to have BLAT at all.
59
+ *
60
+ * Naming it drops a config's `plugins[]` entry for Blat before Desktop's loader
61
+ * sees it, so a config that carries one does not install a second copy beside
62
+ * the bundled one and append its Tools menu items twice. Nothing carries one
63
+ * today: jb2hubs stamps `sequence.metadata.blatDb`, which names the UCSC db an
64
+ * assembly is searchable under and says nothing about loading a plugin. The
65
+ * entry is a guard for the UMD build (`plugins/blat/scripts/build-umd.ts`),
66
+ * which a config can name and which is how Web would pick BLAT up.
67
+ *
68
+ * It lives here beside the shared set rather than in jbrowse-desktop because the
69
+ * two are read together — a surface consulting one and not the other offers an
70
+ * install the loader then drops, which is what Desktop's plugin store and global
71
+ * plugins dialog both did.
72
+ */
73
+ export const desktopVendoredPluginNames = ['Blat'];
74
+ export function dropVendoredPlugins(defs, alsoVendored = []) {
75
+ const vendored = new Set([...vendoredPluginNames, ...alsoVendored]);
76
+ return defs.filter(d => !(isUMDPluginDefinition(d) && vendored.has(d.name)));
77
+ }
78
+ // The two functions below describe a definition by picking the one url it will
79
+ // be loaded from, so both dispatch in loadPlugin's order — CJS, then ESM, then
80
+ // UMD. Keep them in step with it: they are what the plugin trust gate
81
+ // (checkPlugins) reads and what the untrusted-plugin prompt shows, so an order
82
+ // that disagrees with the loader's vets one url and executes another. They once
83
+ // did disagree, and a definition carrying both `umdUrl` and `cjsUrl` was
84
+ // approved on its jbrowse.org umd url while loadPlugin require()d its cjs one.
85
+ // assertSingleKind now rejects such a definition outright; this order is the
86
+ // second half of that guarantee, since the gate runs before the loader does.
87
+ export function pluginDescriptionString(d) {
88
+ if (isCJSPluginDefinition(d)) {
89
+ return `CJS plugin ${d.cjsUrl}`;
90
+ }
91
+ else if (isESMPluginDefinition(d)) {
92
+ return `ESM plugin ${'esmUrl' in d ? d.esmUrl : d.esmLoc.uri}`;
93
+ }
94
+ else if (isUMDPluginDefinition(d)) {
95
+ return `UMD plugin ${d.name}`;
96
+ }
97
+ else if (isStorePluginDefinition(d)) {
98
+ // an unresolved ref, which is what a resolution failure is reported on: it
99
+ // has no url yet, so the store name is the only thing that identifies it
100
+ return `store plugin ${d.storePlugin}`;
101
+ }
102
+ else {
103
+ return 'unknown plugin';
104
+ }
105
+ }
106
+ /**
107
+ * The url a definition loads from, or undefined when it names no loader at all.
108
+ * Comparisons between definitions go through this rather than `pluginUrl`, whose
109
+ * 'unknown url' placeholder is display text: two unloadable definitions are not
110
+ * the same plugin just because neither has a url.
111
+ */
112
+ export function maybePluginUrl(d) {
113
+ if (isCJSPluginDefinition(d)) {
114
+ return d.cjsUrl;
115
+ }
116
+ else if (isESMPluginDefinition(d)) {
117
+ return 'esmUrl' in d ? d.esmUrl : d.esmLoc.uri;
118
+ }
119
+ else if (isUMDPluginDefinition(d)) {
120
+ return 'umdLoc' in d ? d.umdLoc.uri : 'umdUrl' in d ? d.umdUrl : d.url;
121
+ }
122
+ else {
123
+ return undefined;
124
+ }
125
+ }
126
+ export function pluginUrl(d) {
127
+ return maybePluginUrl(d) ?? 'unknown url';
128
+ }
129
+ /**
130
+ * Whether a definition loads from exactly `url` — the question behind "which
131
+ * definition is this loaded plugin", "is this one in the session's list", "which
132
+ * entry does an uninstall remove".
133
+ *
134
+ * The two undefined guards are the whole point, and both were live as
135
+ * `pluginUrl(d) === url` comparisons. A definition naming no loader reads back as
136
+ * the literal `'unknown url'`, so any two of them compared equal: approving one
137
+ * marked every other unloadable definition trusted, and removing one filtered
138
+ * every other unloadable one out of the config. And the url side is absent for a
139
+ * core or global plugin (no install url was recorded), which must match no
140
+ * definition rather than the first url-less one.
141
+ */
142
+ export function isPluginUrl(d, url) {
143
+ const actual = maybePluginUrl(d);
144
+ return actual !== undefined && actual === url;
145
+ }
146
+ export function pluginName(definition) {
147
+ return 'name' in definition ? definition.name : undefined;
148
+ }
149
+ export function pluginDefinitionMetadata(definition) {
150
+ return {
151
+ name: pluginName(definition),
152
+ url: pluginUrl(definition),
153
+ };
154
+ }
155
+ /**
156
+ * How to name a definition to a person — a crash marker saying what was
157
+ * loading, a warning listing what a host did not pass in.
158
+ *
159
+ * A ref that has not been resolved yet has no url and often no `name`, and
160
+ * everything here used to fall through to `pluginUrl`'s 'unknown url' for it:
161
+ * a marker naming nothing, which is the difference between a banner the user
162
+ * can act on and one that says only that something went wrong.
163
+ */
164
+ export function pluginLabel(definition) {
165
+ const name = pluginName(definition) ?? storePluginName(definition);
166
+ const url = maybePluginUrl(definition);
167
+ if (name === undefined) {
168
+ return pluginUrl(definition);
169
+ }
170
+ return url === undefined ? name : `${name} (${url})`;
171
+ }
172
+ /**
173
+ * Whether two definitions describe the same plugin. They can without being
174
+ * identical — a UMD name+url in a config, an esmUrl in the global list, a store
175
+ * ref in one and the pinned definition it resolves to in the other — so a
176
+ * shared store package, a shared name, or a shared url is each enough. All
177
+ * three are optional (an ESM definition carries no name, an unloadable one no
178
+ * url, a hand-written one no package), and a missing field never matches: two
179
+ * definitions are not the same plugin just because neither names one.
180
+ *
181
+ * The store name is checked first because it is the only one of the three that
182
+ * survives resolution intact. A ref and its resolved form share it; they share
183
+ * no url, and a *bare* ref has no `name` until the manifest supplies one — so
184
+ * this clause is doing work even though a resolved definition's `storePlugin`
185
+ * and `name` agree.
186
+ *
187
+ * This is the single answer to "is this plugin already installed" — dedupe
188
+ * across plugin sources, the plugin store's installed-check — so those cannot
189
+ * drift apart and disagree about what is a duplicate.
190
+ */
191
+ export function samePlugin(a, b) {
192
+ const [refA, refB] = [storePluginName(a), storePluginName(b)];
193
+ const [nameA, nameB] = [pluginName(a), pluginName(b)];
194
+ const [urlA, urlB] = [maybePluginUrl(a), maybePluginUrl(b)];
195
+ return ((refA !== undefined && refA === refB) ||
196
+ (nameA !== undefined && nameA === nameB) ||
197
+ (urlA !== undefined && urlA === urlB));
198
+ }
199
+ /**
200
+ * The candidates no definition in `existing` already describes — `dedupePlugins`
201
+ * across two lists whose first one is already settled, for a source loaded after
202
+ * another rather than merged with it.
203
+ */
204
+ export function pluginsNotIn(candidates, existing) {
205
+ return candidates.filter(c => !existing.some(e => samePlugin(e, c)));
206
+ }
207
+ /**
208
+ * Drops later definitions that name a plugin an earlier one already did, so the
209
+ * first source listed wins: a config's own (version-pinned) entry takes
210
+ * precedence over the same plugin from the user's global list.
211
+ */
212
+ export function dedupePlugins(plugins) {
213
+ const kept = [];
214
+ for (const plugin of plugins) {
215
+ if (!kept.some(k => samePlugin(k, plugin))) {
216
+ kept.push(plugin);
217
+ }
218
+ }
219
+ return kept;
220
+ }
@@ -1,40 +1,32 @@
1
1
  import type PluginManager from '../PluginManager.ts';
2
2
  import type { AnyConfigurationModel } from '../configuration/index.ts';
3
- export interface WorkerHandle {
4
- status?: string;
5
- error?: unknown;
6
- on?: (channel: string, callback: (message: unknown) => void) => void;
7
- off?: (channel: string, callback: (message: unknown) => void) => void;
8
- destroy(): void;
9
- call(functionName: string, args?: unknown, options?: {
10
- statusCallback?(message: string): void;
11
- rpcDriverClassName: string;
12
- }): Promise<unknown>;
13
- }
14
- export interface RpcDriverConstructorArgs {
15
- config: AnyConfigurationModel;
16
- }
17
- declare class LazyWorker {
18
- driver: BaseRpcDriver;
19
- workerP?: Promise<WorkerHandle> | undefined;
20
- constructor(driver: BaseRpcDriver);
21
- getWorker(): Promise<WorkerHandle>;
22
- }
3
+ import type RpcMethodType from '../pluggableElementTypes/RpcMethodType.ts';
4
+ import type { StatusCallback } from '../util/progress.ts';
5
+ import type { RpcHandles } from './RpcRegistry.ts';
6
+ /**
7
+ * The method that drops a session's cached adapters, named once because
8
+ * {@link BaseRpcDriver.freeSession} is the only thing that dispatches it.
9
+ */
10
+ export declare const CORE_FREE_RESOURCES = "CoreFreeResources";
23
11
  export default abstract class BaseRpcDriver {
24
- abstract name: string;
25
- private lastWorkerAssignment;
26
- private workerAssignments;
27
- abstract makeWorker(): Promise<WorkerHandle>;
28
- private workerPool?;
12
+ protected pluginManager: PluginManager;
29
13
  config: AnyConfigurationModel;
30
- constructor(args: RpcDriverConstructorArgs);
31
- filterArgs<THING_TYPE>(thing: THING_TYPE, sessionId: string): THING_TYPE;
32
- remoteAbort(sessionId: string, functionName: string, stopTokenId: number): Promise<void>;
33
- createWorkerPool(): LazyWorker[];
34
- getWorkerPool(): LazyWorker[];
35
- getWorker(sessionId: string): Promise<WorkerHandle>;
36
- call(pluginManager: PluginManager, sessionId: string, functionName: string, args: {
37
- statusCallback?: (message: unknown) => void;
38
- }, options?: {}): Promise<unknown>;
14
+ abstract name: string;
15
+ constructor(pluginManager: PluginManager, config: AnyConfigurationModel);
16
+ /**
17
+ * Drop everything this driver holds for a session — the worker-side adapter
18
+ * cache, and whatever bookkeeping the transport keeps alongside it.
19
+ *
20
+ * A driver operation rather than a `call`, because a free has nothing to do on
21
+ * a transport that never ran this session and must not outlive `destroy`;
22
+ * routing it through `call` did both. ADR-086.
23
+ *
24
+ * The base behavior is the main-thread one: run the method in this realm,
25
+ * where `dataAdapterCache` lives. `invoke`, not `execute`, for the reason
26
+ * `MainThreadRpcDriver.transport` uses it.
27
+ */
28
+ freeSession(sessionId: string): Promise<void>;
29
+ destroy(): void;
30
+ call(sessionId: string, functionName: string, args: Record<string, unknown> & RpcHandles): Promise<unknown>;
31
+ protected abstract transport(sessionId: string, rpcMethod: RpcMethodType, serializedArgs: Record<string, unknown>, statusCallback: StatusCallback | undefined): Promise<unknown>;
39
32
  }
40
- export {};
@@ -1,116 +1,83 @@
1
- import { isAlive, isStateTreeNode } from '@jbrowse/mobx-state-tree';
2
- import { readConfObject } from "../configuration/index.js";
3
- import { clamp } from "../util/index.js";
4
- function isCloneable(thing) {
5
- return !(typeof thing === 'function') && !(thing instanceof Error);
6
- }
7
- function detectHardwareConcurrency() {
8
- const mainThread = typeof window !== 'undefined';
9
- const canDetect = mainThread && 'hardwareConcurrency' in window.navigator;
10
- return mainThread && canDetect ? window.navigator.hardwareConcurrency : 1;
11
- }
12
- class LazyWorker {
13
- driver;
14
- workerP;
15
- constructor(driver) {
16
- this.driver = driver;
17
- }
18
- async getWorker() {
19
- if (!this.workerP) {
20
- this.workerP = this.driver.makeWorker().catch((e) => {
21
- this.workerP = undefined;
22
- throw e;
23
- });
24
- }
25
- return this.workerP;
26
- }
27
- }
1
+ import { isStopToken, withStopTokenCheck } from '../util/stopToken.js';
2
+ /**
3
+ * The method that drops a session's cached adapters, named once because
4
+ * {@link BaseRpcDriver.freeSession} is the only thing that dispatches it.
5
+ */
6
+ export const CORE_FREE_RESOURCES = 'CoreFreeResources';
28
7
  export default class BaseRpcDriver {
29
- lastWorkerAssignment = -1;
30
- workerAssignments = new Map();
31
- workerPool;
8
+ pluginManager;
32
9
  config;
33
- constructor(args) {
34
- this.config = args.config;
10
+ // Held, not threaded. `call`, `transport` and `freeSession` each took one as
11
+ // their first parameter and `RpcManager` passed the same object to all of
12
+ // them on every RPC — a driver is built by the manager that owns it, so it
13
+ // can just have one. Holding it is also what lets `Core-extendWorker` fire
14
+ // where a worker boots rather than on the dispatch path. ADR-086.
15
+ constructor(pluginManager, config) {
16
+ this.pluginManager = pluginManager;
17
+ this.config = config;
35
18
  }
36
- filterArgs(thing, sessionId) {
37
- if (thing === null || thing === undefined) {
38
- return thing;
39
- }
40
- const type = typeof thing;
41
- if (type === 'string' || type === 'number' || type === 'boolean') {
42
- return thing;
43
- }
44
- if (type !== 'object') {
45
- return undefined;
46
- }
47
- if (Array.isArray(thing)) {
48
- return thing
49
- .filter(thing => isCloneable(thing))
50
- .map(t => this.filterArgs(t, sessionId));
51
- }
52
- else if (isStateTreeNode(thing) && !isAlive(thing)) {
53
- throw new Error('dead state tree node passed to RPC call');
54
- }
55
- else if (thing instanceof File) {
56
- return thing;
57
- }
58
- else {
59
- return Object.fromEntries(Object.entries(thing)
60
- .filter(e => isCloneable(e[1]))
61
- .map(([k, v]) => [k, this.filterArgs(v, sessionId)]));
62
- }
63
- }
64
- async remoteAbort(sessionId, functionName, stopTokenId) {
65
- const worker = await this.getWorker(sessionId);
66
- await worker.call(functionName, { stopTokenId }, { rpcDriverClassName: this.name });
67
- }
68
- createWorkerPool() {
69
- const hardwareConcurrency = detectHardwareConcurrency();
70
- const workerCount = readConfObject(this.config, 'workerCount') ||
71
- clamp(1, Math.max(1, hardwareConcurrency - 1), 5);
72
- const workers = [];
73
- for (let i = 0; i < workerCount; i++) {
74
- workers.push(new LazyWorker(this));
75
- }
76
- return workers;
19
+ /**
20
+ * Drop everything this driver holds for a session — the worker-side adapter
21
+ * cache, and whatever bookkeeping the transport keeps alongside it.
22
+ *
23
+ * A driver operation rather than a `call`, because a free has nothing to do on
24
+ * a transport that never ran this session and must not outlive `destroy`;
25
+ * routing it through `call` did both. ADR-086.
26
+ *
27
+ * The base behavior is the main-thread one: run the method in this realm,
28
+ * where `dataAdapterCache` lives. `invoke`, not `execute`, for the reason
29
+ * `MainThreadRpcDriver.transport` uses it.
30
+ */
31
+ async freeSession(sessionId) {
32
+ await this.pluginManager
33
+ .getRpcMethodType(CORE_FREE_RESOURCES)
34
+ .invoke({ sessionId });
77
35
  }
78
- getWorkerPool() {
79
- if (!this.workerPool) {
80
- const res = this.createWorkerPool();
81
- this.workerPool = res;
82
- return res;
83
- }
84
- return this.workerPool;
85
- }
86
- async getWorker(sessionId) {
87
- const workers = this.getWorkerPool();
88
- let workerNumber = this.workerAssignments.get(sessionId);
89
- if (workerNumber === undefined) {
90
- const workerAssignment = (this.lastWorkerAssignment + 1) % workers.length;
91
- this.workerAssignments.set(sessionId, workerAssignment);
92
- this.lastWorkerAssignment = workerAssignment;
93
- workerNumber = workerAssignment;
94
- }
95
- return workers[workerNumber].getWorker();
96
- }
97
- async call(pluginManager, sessionId, functionName, args, options = {}) {
36
+ destroy() { }
37
+ async call(sessionId, functionName, args) {
98
38
  if (!sessionId) {
99
39
  throw new TypeError('sessionId is required');
100
40
  }
101
- const unextendedWorker = await this.getWorker(sessionId);
102
- const worker = pluginManager.evaluateExtensionPoint('Core-extendWorker', unextendedWorker);
103
- const rpcMethod = pluginManager.getRpcMethodType(functionName);
104
- if (!rpcMethod) {
105
- throw new Error(`unknown RPC method ${functionName}`);
106
- }
107
- const serializedArgs = await rpcMethod.serializeArguments(args, this.name);
108
- const filteredAndSerializedArgs = this.filterArgs(serializedArgs, sessionId);
109
- const call = await worker.call(functionName, filteredAndSerializedArgs, {
110
- statusCallback: args.statusCallback,
111
- rpcDriverClassName: this.name,
112
- ...options,
113
- });
114
- return rpcMethod.deserializeReturn(call, args, this.name);
41
+ // An RPC method is addressed by string, so a removed or renamed one is not
42
+ // a type error anywhere — it fails here. It fails WELL: `TypeRecord.get`
43
+ // throws naming the method and listing what is registered, which is the
44
+ // "which plugin is missing" answer. No `undefined` check belongs here; one
45
+ // was added and lint called it dead, correctly.
46
+ const rpcMethod = this.pluginManager.getRpcMethodType(functionName);
47
+ // statusCallback is an out-of-band progress handle, not data: each transport
48
+ // wires up its own channel for it, so it must not reach the serialized
49
+ // payload. Everything that does must be structured-cloneable; the worker
50
+ // postMessage clones it and throws on anything that isn't, surfacing bad data
51
+ // at the boundary instead of silently dropping it.
52
+ //
53
+ // Stripped on the way OUT rather than on the way in, so `serializeArguments`
54
+ // can see it. That is not cosmetic: serialization is where the refName map
55
+ // is resolved, and resolving one downloads the adapter's index (and for an
56
+ // in-memory adapter, the whole file). Destructuring the callback off first
57
+ // left that download with nothing to report through — `loadRefNameMap`
58
+ // forwards a `statusCallback` for exactly this and, for every RPC, was
59
+ // handed undefined. The wire payload is identical either way.
60
+ //
61
+ // Serialization is the one long await here, and it is wrapped rather than
62
+ // fenced by hand-placed checks so the check on the FAR side comes with the
63
+ // near one — that is the whole point of `withStopTokenCheck`, and the far
64
+ // one is what was missing. A call whose token was already stopped has
65
+ // nothing to deliver to, so refuse it rather than serializing args, waking a
66
+ // worker and racing a stop notification against the call it means to cancel;
67
+ // and a stop landing DURING serialization had nowhere to be seen at all,
68
+ // because the broadcast it fires reaches only *booted* workers and on a
69
+ // driver's first call `LazyWorker.workerP` is undefined until `transport`
70
+ // reaches `getWorker`. The worker never learned the token was stopped and
71
+ // ground the fetch to completion. SharedArrayBuffer tokens see the stop
72
+ // through shared memory regardless; this is the string-token path, which is
73
+ // every deployment we ship — `stopToken.ts`, "Which path runs where".
74
+ //
75
+ // Callers already treat an abort as the ordinary outcome of a superseded
76
+ // fetch.
77
+ const stopToken = isStopToken(args.stopToken) ? args.stopToken : undefined;
78
+ const { statusCallback } = args;
79
+ const { statusCallback: _outOfBand, ...serializedArgs } = await withStopTokenCheck(stopToken, () => rpcMethod.serializeArguments(args));
80
+ const result = await this.transport(sessionId, rpcMethod, serializedArgs, statusCallback);
81
+ return rpcMethod.deserializeReturn(result, args);
115
82
  }
116
83
  }
@@ -1,14 +1,13 @@
1
1
  import BaseRpcDriver from './BaseRpcDriver.ts';
2
- import type { RpcDriverConstructorArgs } from './BaseRpcDriver.ts';
3
- import type PluginManager from '../PluginManager.ts';
4
- declare class DummyHandle {
5
- destroy(): void;
6
- call(_functionName: string, _filteredArgs?: Record<string, unknown>, _options?: {}): Promise<unknown>;
7
- }
2
+ import type RpcMethodType from '../pluggableElementTypes/RpcMethodType.ts';
3
+ import type { StatusCallback } from '../util/progress.ts';
4
+ /**
5
+ * RPC driver that runs RPC functions in-band on the main thread. It owns no
6
+ * worker pool, so `destroy` stays the BaseRpcDriver no-op and `freeSession`
7
+ * stays that class's in-realm free — the adapter cache this driver fills is the
8
+ * main thread's own.
9
+ */
8
10
  export default class MainThreadRpcDriver extends BaseRpcDriver {
9
11
  name: string;
10
- makeWorker: () => Promise<DummyHandle>;
11
- constructor(args: RpcDriverConstructorArgs);
12
- call(pm: PluginManager, sessionId: string, funcName: string, args: Record<string, unknown>): Promise<unknown>;
12
+ protected transport(_sessionId: string, rpcMethod: RpcMethodType, serializedArgs: Record<string, unknown>, statusCallback: StatusCallback | undefined): Promise<unknown>;
13
13
  }
14
- export {};
@@ -1,33 +1,22 @@
1
- import BaseRpcDriver from "./BaseRpcDriver.js";
2
- class DummyHandle {
3
- destroy() { }
4
- async call(_functionName, _filteredArgs, _options = {}) {
5
- return undefined;
6
- }
7
- }
1
+ import BaseRpcDriver from './BaseRpcDriver.js';
2
+ /**
3
+ * RPC driver that runs RPC functions in-band on the main thread. It owns no
4
+ * worker pool, so `destroy` stays the BaseRpcDriver no-op and `freeSession`
5
+ * stays that class's in-realm free — the adapter cache this driver fills is the
6
+ * main thread's own.
7
+ */
8
8
  export default class MainThreadRpcDriver extends BaseRpcDriver {
9
9
  name = 'MainThreadRpcDriver';
10
- makeWorker;
11
- constructor(args) {
12
- super(args);
13
- this.makeWorker = async () => new DummyHandle();
14
- }
15
- async call(pm, sessionId, funcName, args) {
16
- if (!sessionId) {
17
- throw new TypeError('sessionId is required');
18
- }
19
- const rpcMethod = pm.getRpcMethodType(funcName);
20
- if (!rpcMethod) {
21
- throw new Error(`unknown RPC method ${funcName}`);
22
- }
23
- if (rpcMethod.supportsDirectExecution()) {
24
- const result = await rpcMethod.executeDirect(args);
25
- if (result !== undefined) {
26
- return result;
27
- }
28
- }
29
- const serializedArgs = await rpcMethod.serializeArguments(args, this.name);
30
- const result = await rpcMethod.execute(serializedArgs, this.name);
31
- return rpcMethod.deserializeReturn(result, args, this.name);
10
+ async transport(_sessionId, rpcMethod, serializedArgs, statusCallback) {
11
+ // re-attach the out-of-band statusCallback that BaseRpcDriver.call split off,
12
+ // mirroring how the worker re-wires it on the far side of postMessage —
13
+ // including the case where there is none, which `wrapForRpc` answers by
14
+ // adding no key at all. Spreading `statusCallback: undefined` in would leave
15
+ // the two drivers handing `execute` bags that differ by a key, which is the
16
+ // kind of difference nothing tests and something eventually reads.
17
+ //
18
+ // `invoke`, not `execute` — it is the entry point that deserializes the
19
+ // arguments first, and the worker binds the same one
20
+ return rpcMethod.invoke(statusCallback ? { ...serializedArgs, statusCallback } : serializedArgs);
32
21
  }
33
22
  }
@@ -0,0 +1,38 @@
1
+ import type { ErrorObject } from './serializeError/index.ts';
2
+ type Listener = (arg: unknown) => void;
3
+ interface RpcMessageData {
4
+ uid: string;
5
+ libRpc?: true;
6
+ error?: string | ErrorObject;
7
+ eventName?: string;
8
+ data?: unknown;
9
+ }
10
+ interface PendingCall {
11
+ resolve: (data: unknown) => void;
12
+ reject: (error: Error) => void;
13
+ }
14
+ export default class RpcClient {
15
+ worker: Worker;
16
+ pending: Map<string, PendingCall>;
17
+ private events;
18
+ private counter;
19
+ constructor(worker: Worker);
20
+ on(event: string, listener: Listener): this;
21
+ off(event: string, listener: Listener): this;
22
+ emit(event: string, data: unknown): this;
23
+ protected handler(e: MessageEvent<RpcMessageData>): void;
24
+ destroy(): void;
25
+ private rejectAllPending;
26
+ protected catch(e: ErrorEvent): void;
27
+ protected reject(uid: string, error: string | ErrorObject): void;
28
+ protected resolve(uid: string, data: unknown): void;
29
+ /**
30
+ * Tell this worker that a stop token has been stopped, so the calls running
31
+ * there see it at their next await boundary and drop their in-flight reads.
32
+ * Fire-and-forget: it settles no pending call, and a worker holding nothing
33
+ * under that id ignores it.
34
+ */
35
+ notifyStopToken(id: string): void;
36
+ call(method: string, data: unknown): Promise<unknown>;
37
+ }
38
+ export {};