@jbrowse/core 4.3.0 → 5.0.0-beta.10

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1265) hide show
  1. package/README.md +1994 -0
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +14 -3
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +36 -23
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +10 -7
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +124 -21
  6. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.d.ts +2 -8
  7. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js +4 -4
  8. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts +1 -1
  9. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js +2 -5
  10. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.d.ts +1 -1
  11. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js +4 -4
  12. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.d.ts +12 -1
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +19 -5
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +18 -23
  16. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.d.ts +1 -1
  17. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +19 -40
  18. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +9 -6
  19. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +33 -30
  20. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.d.ts +11 -0
  21. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.js +11 -0
  22. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
  23. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
  24. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.d.ts +8 -0
  25. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.js +24 -0
  26. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
  27. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
  28. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
  29. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +19 -0
  30. package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.d.ts +4 -0
  31. package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.js +17 -0
  32. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +5 -3
  33. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +8 -6
  34. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
  35. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
  36. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +7 -2
  37. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +15 -20
  38. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.d.ts +16 -0
  39. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.js +50 -0
  40. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +0 -1
  41. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +9 -10
  42. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
  43. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
  44. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
  45. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +35 -24
  46. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
  47. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
  48. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +3 -3
  49. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
  50. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
  51. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
  52. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
  53. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
  54. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
  55. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
  56. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
  57. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
  58. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
  59. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
  60. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
  61. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
  62. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
  63. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
  64. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
  65. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
  66. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
  67. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
  68. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
  69. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
  70. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
  71. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +20 -0
  72. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
  73. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
  74. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
  75. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +62 -63
  76. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +69 -59
  77. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
  78. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
  79. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
  80. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
  81. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
  82. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
  83. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
  84. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
  85. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
  86. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
  87. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
  88. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
  89. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
  90. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
  91. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
  92. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
  93. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
  94. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
  95. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
  96. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
  97. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
  98. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
  99. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
  100. package/esm/BaseFeatureWidget/configSchema.d.ts +1 -1
  101. package/esm/BaseFeatureWidget/configSchema.js +1 -1
  102. package/esm/BaseFeatureWidget/formatDetails.d.ts +22 -0
  103. package/esm/BaseFeatureWidget/formatDetails.js +82 -0
  104. package/esm/BaseFeatureWidget/index.d.ts +4 -1
  105. package/esm/BaseFeatureWidget/index.js +2 -2
  106. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +102 -71
  107. package/esm/BaseFeatureWidget/stateModelFactory.js +162 -63
  108. package/esm/BaseFeatureWidget/types.d.ts +15 -8
  109. package/esm/BaseFeatureWidget/util.d.ts +2 -37
  110. package/esm/BaseFeatureWidget/util.js +4 -85
  111. package/esm/CorePlugin.js +12 -7
  112. package/esm/PhasedScheduler.d.ts +4 -2
  113. package/esm/PhasedScheduler.js +18 -2
  114. package/esm/Plugin.d.ts +6 -1
  115. package/esm/Plugin.js +7 -0
  116. package/esm/PluginLoader.d.ts +55 -44
  117. package/esm/PluginLoader.js +290 -90
  118. package/esm/PluginManager.d.ts +476 -57
  119. package/esm/PluginManager.js +480 -91
  120. package/esm/ReExports/MuiDataGridReExports.d.ts +3 -2
  121. package/esm/ReExports/MuiDataGridReExports.js +58 -130
  122. package/esm/ReExports/MuiReExports.d.ts +3 -134
  123. package/esm/ReExports/MuiReExports.js +43 -16
  124. package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
  125. package/esm/ReExports/MuiStylesReExports.js +55 -0
  126. package/esm/ReExports/coreModules.generated.d.ts +2 -0
  127. package/esm/ReExports/coreModules.generated.js +528 -0
  128. package/esm/ReExports/coreWorkerModules.generated.d.ts +2 -0
  129. package/esm/ReExports/coreWorkerModules.generated.js +488 -0
  130. package/esm/ReExports/frameworkModules.d.ts +2 -0
  131. package/esm/ReExports/frameworkModules.js +68 -0
  132. package/esm/ReExports/frameworkShared.d.ts +12 -0
  133. package/esm/ReExports/frameworkShared.js +16 -0
  134. package/esm/ReExports/frameworkWorkerModules.generated.d.ts +2 -0
  135. package/esm/ReExports/frameworkWorkerModules.generated.js +130 -0
  136. package/esm/ReExports/lazify.d.ts +2 -2
  137. package/esm/ReExports/lazify.js +16 -3
  138. package/esm/ReExports/list.js +433 -160
  139. package/esm/ReExports/modules.d.ts +1 -1
  140. package/esm/ReExports/modules.js +10 -146
  141. package/esm/ReExports/muiComponentNames.d.ts +18 -0
  142. package/esm/ReExports/muiComponentNames.js +130 -0
  143. package/esm/ReExports/registry.d.ts +3 -0
  144. package/esm/ReExports/registry.js +46 -0
  145. package/esm/ReExports/uiStub.d.ts +3 -0
  146. package/esm/ReExports/uiStub.js +33 -0
  147. package/esm/ReExports/workerModules.d.ts +2 -0
  148. package/esm/ReExports/workerModules.js +11 -0
  149. package/esm/TextSearch/BaseResults.d.ts +20 -21
  150. package/esm/TextSearch/BaseResults.js +8 -33
  151. package/esm/TextSearch/TextSearchManager.d.ts +30 -36
  152. package/esm/TextSearch/TextSearchManager.js +138 -44
  153. package/esm/TextSearch/places.d.ts +12 -0
  154. package/esm/TextSearch/places.js +94 -0
  155. package/esm/assemblyManager/assembly.d.ts +310 -35
  156. package/esm/assemblyManager/assembly.js +554 -263
  157. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  158. package/esm/assemblyManager/assemblyAdapters.js +24 -0
  159. package/esm/assemblyManager/assemblyConfigSchema.d.ts +135 -19
  160. package/esm/assemblyManager/assemblyConfigSchema.js +205 -23
  161. package/esm/assemblyManager/assemblyManager.d.ts +586 -323
  162. package/esm/assemblyManager/assemblyManager.js +352 -51
  163. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +39 -0
  164. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +114 -0
  165. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  166. package/esm/assemblyManager/geneticCodes.js +44 -0
  167. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +19 -0
  168. package/esm/assemblyManager/getSequenceAdapterConfig.js +22 -0
  169. package/esm/assemblyManager/index.d.ts +1 -1
  170. package/esm/assemblyManager/index.js +2 -2
  171. package/esm/assemblyManager/indexAssemblyNames.d.ts +9 -0
  172. package/esm/assemblyManager/indexAssemblyNames.js +22 -0
  173. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  174. package/esm/assemblyManager/loadRefNameMap.js +75 -0
  175. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  176. package/esm/assemblyManager/refNameColors.js +32 -0
  177. package/esm/assemblyManager/refNameMapKey.d.ts +7 -0
  178. package/esm/assemblyManager/refNameMapKey.js +12 -0
  179. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  180. package/esm/assemblyManager/refNameMaps.js +87 -0
  181. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  182. package/esm/assemblyManager/refNameMismatch.js +66 -0
  183. package/esm/checkPlugins.d.ts +13 -0
  184. package/esm/checkPlugins.js +98 -0
  185. package/esm/configuration/bamIndexFields.d.ts +49 -0
  186. package/esm/configuration/bamIndexFields.js +41 -0
  187. package/esm/configuration/configurationSchema.d.ts +194 -29
  188. package/esm/configuration/configurationSchema.js +439 -145
  189. package/esm/configuration/configurationSchemaUnion.d.ts +39 -0
  190. package/esm/configuration/configurationSchemaUnion.js +56 -0
  191. package/esm/configuration/configurationSlot.d.ts +373 -30
  192. package/esm/configuration/configurationSlot.js +231 -224
  193. package/esm/configuration/fillLocations.d.ts +14 -0
  194. package/esm/configuration/fillLocations.js +14 -0
  195. package/esm/configuration/formatAboutConfigSchema.d.ts +41 -0
  196. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  197. package/esm/configuration/formatDetailsConfigSchema.d.ts +54 -0
  198. package/esm/configuration/formatDetailsConfigSchema.js +87 -0
  199. package/esm/configuration/fullConfSnapshot.d.ts +13 -0
  200. package/esm/configuration/fullConfSnapshot.js +44 -0
  201. package/esm/configuration/getConf.d.ts +92 -0
  202. package/esm/configuration/getConf.js +141 -0
  203. package/esm/configuration/index.d.ts +32 -3
  204. package/esm/configuration/index.js +27 -2
  205. package/esm/configuration/indexType.d.ts +26 -0
  206. package/esm/configuration/indexType.js +38 -0
  207. package/esm/configuration/mergeFormatCallbacks.d.ts +14 -0
  208. package/esm/configuration/mergeFormatCallbacks.js +27 -0
  209. package/esm/configuration/readConfObject.d.ts +34 -0
  210. package/esm/configuration/readConfObject.js +118 -0
  211. package/esm/configuration/requirements.d.ts +37 -0
  212. package/esm/configuration/requirements.js +88 -0
  213. package/esm/configuration/schemaRegistry.d.ts +52 -0
  214. package/esm/configuration/schemaRegistry.js +48 -0
  215. package/esm/configuration/schemaTypes.d.ts +39 -0
  216. package/esm/configuration/schemaTypes.js +105 -0
  217. package/esm/configuration/slotFacade.d.ts +65 -0
  218. package/esm/configuration/slotFacade.js +110 -0
  219. package/esm/configuration/slotValueUtils.d.ts +17 -0
  220. package/esm/configuration/slotValueUtils.js +25 -0
  221. package/esm/configuration/snapshotPreprocess.d.ts +43 -0
  222. package/esm/configuration/snapshotPreprocess.js +161 -0
  223. package/esm/configuration/tabixIndexFields.d.ts +70 -0
  224. package/esm/configuration/tabixIndexFields.js +62 -0
  225. package/esm/configuration/tabixShorthand.d.ts +51 -0
  226. package/esm/configuration/tabixShorthand.js +72 -0
  227. package/esm/configuration/types.d.ts +315 -13
  228. package/esm/configuration/uriShorthand.d.ts +9 -0
  229. package/esm/configuration/uriShorthand.js +16 -0
  230. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +19 -11
  231. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +19 -18
  232. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +158 -7
  233. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +164 -29
  234. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  235. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  236. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  237. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  238. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  239. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  240. package/esm/data_adapters/BaseAdapter/featureDensity.d.ts +40 -0
  241. package/esm/data_adapters/BaseAdapter/featureDensity.js +31 -0
  242. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  243. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  244. package/esm/data_adapters/BaseAdapter/index.d.ts +28 -6
  245. package/esm/data_adapters/BaseAdapter/index.js +6 -5
  246. package/esm/data_adapters/BaseAdapter/rowSources.d.ts +37 -0
  247. package/esm/data_adapters/BaseAdapter/rowSources.js +7 -0
  248. package/esm/data_adapters/BaseAdapter/stats.d.ts +37 -5
  249. package/esm/data_adapters/BaseAdapter/stats.js +89 -24
  250. package/esm/data_adapters/BaseAdapter/types.d.ts +11 -13
  251. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  252. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  253. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  254. package/esm/data_adapters/BaseAdapter/zoomRange.d.ts +10 -0
  255. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  256. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +5 -5
  257. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +34 -6
  258. package/esm/data_adapters/CytobandAdapter/configSchema.js +47 -17
  259. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  260. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  261. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  262. package/esm/data_adapters/dataAdapterCache.d.ts +53 -2
  263. package/esm/data_adapters/dataAdapterCache.js +99 -25
  264. package/esm/data_adapters/getFeatureAdapter.d.ts +24 -0
  265. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  266. package/esm/data_adapters/getSequenceSubAdapter.d.ts +19 -0
  267. package/esm/data_adapters/getSequenceSubAdapter.js +42 -0
  268. package/esm/pluggableElementTypes/AdapterType.d.ts +57 -7
  269. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  270. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  271. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  272. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  273. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  274. package/esm/pluggableElementTypes/DisplayType.d.ts +54 -14
  275. package/esm/pluggableElementTypes/DisplayType.js +30 -7
  276. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  277. package/esm/pluggableElementTypes/LazyStateModelElement.d.ts +32 -0
  278. package/esm/pluggableElementTypes/LazyStateModelElement.js +77 -0
  279. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +11 -0
  280. package/esm/pluggableElementTypes/PluggableElementBase.js +11 -0
  281. package/esm/pluggableElementTypes/RpcMethodType.d.ts +142 -12
  282. package/esm/pluggableElementTypes/RpcMethodType.js +279 -98
  283. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +18 -9
  284. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  285. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  286. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  287. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  288. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  289. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +7 -7
  290. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  291. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  292. package/esm/pluggableElementTypes/TrackType.js +1 -1
  293. package/esm/pluggableElementTypes/ViewType.d.ts +22 -5
  294. package/esm/pluggableElementTypes/ViewType.js +40 -5
  295. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  296. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  297. package/esm/pluggableElementTypes/addMenuItems.d.ts +88 -0
  298. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  299. package/esm/pluggableElementTypes/extendElementType.d.ts +29 -0
  300. package/esm/pluggableElementTypes/extendElementType.js +72 -0
  301. package/esm/pluggableElementTypes/index.d.ts +8 -7
  302. package/esm/pluggableElementTypes/index.js +24 -14
  303. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +80 -15
  304. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  305. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +643 -84
  306. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +230 -60
  307. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +246 -37
  308. package/esm/pluggableElementTypes/models/BaseTrackModel.js +416 -107
  309. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +236 -16
  310. package/esm/pluggableElementTypes/models/BaseViewModel.js +154 -16
  311. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +169 -25
  312. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  313. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +178 -0
  314. package/esm/pluggableElementTypes/models/assertDisplayContract.js +239 -0
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  1021. package/esm/util/revlist.js +14 -0
  1022. package/esm/util/rowStackGeometry.d.ts +66 -0
  1023. package/esm/util/rowStackGeometry.js +70 -0
  1024. package/esm/util/rpc.d.ts +16 -1
  1025. package/esm/util/rpc.js +12 -1
  1026. package/esm/util/rxjs.d.ts +30 -2
  1027. package/esm/util/rxjs.js +85 -10
  1028. package/esm/util/sameStrings.d.ts +16 -0
  1029. package/esm/util/sameStrings.js +20 -0
  1030. package/esm/util/samplesTsv.d.ts +49 -0
  1031. package/esm/util/samplesTsv.js +86 -0
  1032. package/esm/util/scheduleDetachedDestroy.d.ts +18 -0
  1033. package/esm/util/scheduleDetachedDestroy.js +24 -0
  1034. package/esm/util/scrollLatch.d.ts +5 -0
  1035. package/esm/util/scrollLatch.js +67 -0
  1036. package/esm/util/selectEncodedFeature.d.ts +16 -0
  1037. package/esm/util/selectEncodedFeature.js +34 -0
  1038. package/esm/util/selectNamedRegions.d.ts +136 -0
  1039. package/esm/util/selectNamedRegions.js +222 -0
  1040. package/esm/util/seqUtils.d.ts +17 -0
  1041. package/esm/util/seqUtils.js +80 -0
  1042. package/esm/util/sessionServices.d.ts +29 -0
  1043. package/esm/util/sessionServices.js +46 -0
  1044. package/esm/util/sessionSharing.d.ts +40 -0
  1045. package/esm/util/sessionSharing.js +154 -0
  1046. package/esm/util/sessionStorage.d.ts +1 -0
  1047. package/esm/util/sessionStorage.js +15 -0
  1048. package/esm/util/setStackTraceLimit.d.ts +6 -0
  1049. package/esm/util/setStackTraceLimit.js +20 -0
  1050. package/esm/util/shapeNameList.d.ts +2 -0
  1051. package/esm/util/shapeNameList.js +6 -0
  1052. package/esm/util/shapeNames.d.ts +7 -0
  1053. package/esm/util/shapeNames.js +11 -0
  1054. package/esm/util/simpleFeature.d.ts +111 -4
  1055. package/esm/util/simpleFeature.js +181 -29
  1056. package/esm/util/springAnimate.d.ts +20 -0
  1057. package/esm/util/springAnimate.js +80 -0
  1058. package/esm/util/starFusion.d.ts +26 -0
  1059. package/esm/util/starFusion.js +37 -0
  1060. package/esm/util/stats.d.ts +25 -2
  1061. package/esm/util/stats.js +39 -8
  1062. package/esm/util/stepTables.d.ts +82 -0
  1063. package/esm/util/stepTables.js +243 -0
  1064. package/esm/util/stringUtils.d.ts +5 -0
  1065. package/esm/util/stringUtils.js +34 -0
  1066. package/esm/util/svAlt.d.ts +145 -0
  1067. package/esm/util/svAlt.js +364 -0
  1068. package/esm/util/svgColorProps.d.ts +18 -0
  1069. package/esm/util/svgColorProps.js +55 -0
  1070. package/esm/util/systemColorScheme.d.ts +12 -0
  1071. package/esm/util/systemColorScheme.js +27 -0
  1072. package/esm/util/tabix.d.ts +125 -0
  1073. package/esm/util/tabix.js +148 -0
  1074. package/esm/util/tags.d.ts +2 -0
  1075. package/esm/util/tags.js +5 -0
  1076. package/esm/util/temporaryAssembly.d.ts +21 -0
  1077. package/esm/util/temporaryAssembly.js +29 -0
  1078. package/esm/util/thresholdScale.d.ts +91 -0
  1079. package/esm/util/thresholdScale.js +166 -0
  1080. package/esm/util/tickLabels.d.ts +36 -0
  1081. package/esm/util/tickLabels.js +45 -0
  1082. package/esm/util/timeGate.d.ts +25 -0
  1083. package/esm/util/timeGate.js +78 -0
  1084. package/esm/util/trackConfigDelta.d.ts +84 -0
  1085. package/esm/util/trackConfigDelta.js +206 -0
  1086. package/esm/util/tracks.d.ts +431 -30
  1087. package/esm/util/tracks.js +952 -185
  1088. package/esm/util/translateTranscript.d.ts +44 -0
  1089. package/esm/util/translateTranscript.js +102 -0
  1090. package/esm/util/tss-react/cssAndCx.js +11 -66
  1091. package/esm/util/tss-react/index.d.ts +11 -2
  1092. package/esm/util/tss-react/index.js +9 -2
  1093. package/esm/util/tss-react/makeStyles.js +7 -4
  1094. package/esm/util/tss-react/mergeClasses.js +1 -0
  1095. package/esm/util/tss-react/tools/classnames.d.ts +3 -0
  1096. package/esm/util/tss-react/tools/classnames.js +3 -0
  1097. package/esm/util/tss-react/tools/getDependencyArrayRef.d.ts +18 -0
  1098. package/esm/util/tss-react/tools/getDependencyArrayRef.js +19 -0
  1099. package/esm/util/tss-react/types.d.ts +1 -1
  1100. package/esm/util/tss-react/types.js +1 -6
  1101. package/esm/util/types/ElementId.js +1 -1
  1102. package/esm/util/types/data.d.ts +73 -0
  1103. package/esm/util/types/data.js +41 -0
  1104. package/esm/util/types/index.d.ts +459 -121
  1105. package/esm/util/types/index.js +96 -64
  1106. package/esm/util/types/isAny.d.ts +11 -0
  1107. package/esm/util/types/isAny.js +1 -0
  1108. package/esm/util/types/mst.d.ts +74 -47
  1109. package/esm/util/types/mst.js +31 -22
  1110. package/esm/util/types/predicate.d.ts +9 -0
  1111. package/esm/util/types/predicate.js +1 -0
  1112. package/esm/util/types/renameIds.d.ts +1 -0
  1113. package/esm/util/types/renameIds.js +29 -0
  1114. package/esm/util/types/renderingServices.d.ts +16 -0
  1115. package/esm/util/types/renderingServices.js +1 -0
  1116. package/esm/util/types/services.d.ts +55 -0
  1117. package/esm/util/types/services.js +10 -0
  1118. package/esm/util/types/util.d.ts +8 -2
  1119. package/esm/util/unknownSnapshotKeys.d.ts +51 -0
  1120. package/esm/util/unknownSnapshotKeys.js +82 -0
  1121. package/esm/util/unzip.d.ts +1 -0
  1122. package/esm/util/unzip.js +6 -0
  1123. package/esm/util/useEventCallback.d.ts +1 -0
  1124. package/esm/util/useEventCallback.js +16 -0
  1125. package/esm/util/useFeatureSequence.d.ts +13 -7
  1126. package/esm/util/useFeatureSequence.js +55 -77
  1127. package/esm/util/useFetch.d.ts +55 -0
  1128. package/esm/util/useFetch.js +197 -0
  1129. package/esm/util/useFetchPlugins.d.ts +16 -0
  1130. package/esm/util/useFetchPlugins.js +18 -0
  1131. package/esm/util/useMeasure.d.ts +11 -1
  1132. package/esm/util/useMeasure.js +20 -6
  1133. package/esm/util/usePanZoom.d.ts +75 -0
  1134. package/esm/util/usePanZoom.js +175 -0
  1135. package/esm/util/usePanelVirtualScroll.d.ts +9 -0
  1136. package/esm/util/usePanelVirtualScroll.js +15 -0
  1137. package/esm/util/usePointerDrag.d.ts +37 -0
  1138. package/esm/util/usePointerDrag.js +61 -0
  1139. package/esm/util/useRafCommit.d.ts +4 -0
  1140. package/esm/util/useRafCommit.js +50 -0
  1141. package/esm/util/useResizeDrag.d.ts +91 -0
  1142. package/esm/util/useResizeDrag.js +105 -0
  1143. package/esm/util/useRowVirtualScroll.d.ts +9 -0
  1144. package/esm/util/useRowVirtualScroll.js +22 -0
  1145. package/esm/util/useVirtualScrollWheel.d.ts +23 -0
  1146. package/esm/util/useVirtualScrollWheel.js +74 -0
  1147. package/esm/util/viewHighlights.d.ts +3 -0
  1148. package/esm/util/viewHighlights.js +5 -0
  1149. package/esm/util/viewStatus.d.ts +90 -0
  1150. package/esm/util/viewStatus.js +54 -0
  1151. package/esm/util/virtualRange.d.ts +36 -0
  1152. package/esm/util/virtualRange.js +26 -0
  1153. package/esm/util/webStorage.d.ts +26 -0
  1154. package/esm/util/webStorage.js +92 -0
  1155. package/esm/util/wheelZoom.d.ts +65 -0
  1156. package/esm/util/wheelZoom.js +297 -0
  1157. package/esm/util/whenViewSettled.d.ts +74 -0
  1158. package/esm/util/whenViewSettled.js +77 -0
  1159. package/esm/util/withFeatureDetails.d.ts +34 -0
  1160. package/esm/util/withFeatureDetails.js +59 -0
  1161. package/esm/util/withLaunchInput.d.ts +174 -0
  1162. package/esm/util/withLaunchInput.js +274 -0
  1163. package/package.json +290 -820
  1164. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +0 -2
  1165. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +0 -14
  1166. package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +0 -7
  1167. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +0 -80
  1168. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.js +0 -583
  1169. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +0 -141
  1170. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.js +0 -1116
  1171. package/esm/ReExports/BaseFeatureDetails.d.ts +0 -1
  1172. package/esm/ReExports/BaseFeatureDetails.js +0 -9
  1173. package/esm/ReExports/DataGrid.d.ts +0 -1
  1174. package/esm/ReExports/DataGrid.js +0 -1
  1175. package/esm/ReExports/index.d.ts +0 -1
  1176. package/esm/ReExports/index.js +0 -1
  1177. package/esm/configuration/util.d.ts +0 -10
  1178. package/esm/configuration/util.js +0 -123
  1179. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
  1180. package/esm/data_adapters/util.d.ts +0 -1
  1181. package/esm/data_adapters/util.js +0 -6
  1182. package/esm/pluggableElementTypes/GlyphType.d.ts +0 -43
  1183. package/esm/pluggableElementTypes/GlyphType.js +0 -18
  1184. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +0 -5
  1185. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +0 -17
  1186. package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +0 -52
  1187. package/esm/pluggableElementTypes/renderers/BoxRendererType.js +0 -78
  1188. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +0 -4
  1189. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +0 -4
  1190. package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -58
  1191. package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +0 -77
  1192. package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +0 -31
  1193. package/esm/pluggableElementTypes/renderers/LayoutSession.js +0 -40
  1194. package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
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  1198. package/esm/pluggableElementTypes/renderers/index.d.ts +0 -6
  1199. package/esm/pluggableElementTypes/renderers/index.js +0 -6
  1200. package/esm/pluggableElementTypes/renderers/util.d.ts +0 -3
  1201. package/esm/pluggableElementTypes/renderers/util.js +0 -14
  1202. package/esm/rpc/baseRpcConfig.d.ts +0 -8
  1203. package/esm/rpc/baseRpcConfig.js +0 -10
  1204. package/esm/rpc/mainThreadRpcConfig.d.ts +0 -8
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  1208. package/esm/rpc/methods/CoreGetFeatureDetails.d.ts +0 -11
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  1218. package/esm/rpc/webWorkerRpcConfig.d.ts +0 -8
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  1220. package/esm/ui/MenuButton.d.ts +0 -1
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  1222. package/esm/ui/MenuItems.d.ts +0 -15
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  1224. package/esm/ui/useEvent.d.ts +0 -1
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  1232. package/esm/util/layouts/BaseLayout.d.ts +0 -30
  1233. package/esm/util/layouts/MultiLayout.d.ts +0 -12
  1234. package/esm/util/layouts/MultiLayout.js +0 -40
  1235. package/esm/util/layouts/PileupLayout.d.ts +0 -41
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  1243. package/esm/util/map-obj/index.d.ts +0 -13
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  1245. package/esm/util/nextTick.d.ts +0 -1
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  1247. package/esm/util/offscreenCanvasGetSerializingSvg.d.ts +0 -5
  1248. package/esm/util/offscreenCanvasGetSerializingSvg.js +0 -9
  1249. package/esm/util/offscreenCanvasUtils.d.ts +0 -12
  1250. package/esm/util/offscreenCanvasUtils.js +0 -19
  1251. package/esm/util/renderToAbstractCanvas.d.ts +0 -17
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  1253. package/esm/util/stopToken.d.ts +0 -19
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  1255. package/esm/util/transferables.d.ts +0 -2
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  1257. package/esm/util/tss-react/mui/index.d.ts +0 -1
  1258. package/esm/util/tss-react/mui/index.js +0 -1
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  1262. package/esm/util/when.js +0 -1
  1263. /package/esm/{BaseFeatureWidget/BaseFeatureDetail/types.js → data_adapters/BaseAdapter/CytobandAdapter.js} +0 -0
  1264. /package/esm/data_adapters/BaseAdapter/{BaseOptions.js → zoomRange.js} +0 -0
  1265. /package/esm/{util/layouts/BaseLayout.js → rpc/RpcRegistry.js} +0 -0
@@ -1,64 +1,75 @@
1
1
  import type { PluginConstructor } from './Plugin.ts';
2
- export interface UMDLocPluginDefinition {
3
- umdLoc: {
4
- uri: string;
5
- baseUri?: string;
6
- };
7
- name: string;
8
- }
9
- export interface UMDUrlPluginDefinition {
10
- umdUrl: string;
11
- name: string;
12
- }
13
- export interface LegacyUMDPluginDefinition {
14
- url: string;
15
- name: string;
16
- }
17
- type UMDPluginDefinition = UMDLocPluginDefinition | UMDUrlPluginDefinition;
18
- export declare function isUMDPluginDefinition(def: PluginDefinition): def is UMDPluginDefinition | LegacyUMDPluginDefinition;
19
- export interface ESMLocPluginDefinition {
20
- esmLoc: {
21
- uri: string;
22
- baseUri?: string;
23
- };
24
- }
25
- export interface ESMUrlPluginDefinition {
26
- esmUrl: string;
27
- }
28
- export type ESMPluginDefinition = ESMLocPluginDefinition | ESMUrlPluginDefinition;
29
- export declare function isESMPluginDefinition(def: PluginDefinition): def is ESMPluginDefinition;
30
- export interface CJSPluginDefinition {
31
- cjsUrl: string;
32
- }
33
- export declare function isCJSPluginDefinition(def: PluginDefinition): def is CJSPluginDefinition;
34
- export type PluginDefinition = UMDUrlPluginDefinition | UMDLocPluginDefinition | LegacyUMDPluginDefinition | ESMLocPluginDefinition | ESMUrlPluginDefinition | CJSPluginDefinition;
2
+ import type { ESMPluginDefinition, LegacyUMDPluginDefinition, PluginDefinition, UMDPluginDefinition } from './pluginDefinitions.ts';
35
3
  export interface PluginRecord {
36
4
  plugin: PluginConstructor;
37
5
  definition: PluginDefinition;
38
6
  }
7
+ export type ReExportRegistryLoader = () => Promise<{
8
+ default: Record<string, unknown>;
9
+ }>;
39
10
  export interface LoadedPlugin {
40
11
  default: PluginConstructor;
41
12
  }
42
- export declare function pluginDescriptionString(d: PluginDefinition): string;
43
- export declare function pluginUrl(d: PluginDefinition): any;
13
+ /** A definition that could not be loaded, kept with the reason it failed */
14
+ export interface PluginLoadFailure {
15
+ definition: PluginDefinition;
16
+ error: unknown;
17
+ }
18
+ export declare function workerScriptLoadMessage(scriptUrl: string, error: unknown): string;
19
+ /**
20
+ * The registry has to be published before a plugin bundle runs, but not before
21
+ * it downloads, so each bundle is preloaded while the registry is fetched.
22
+ * Skipped under the cache-buster, whose query string differs per request.
23
+ *
24
+ * Exported for a worker told its plugins ahead of its boot configuration.
25
+ */
26
+ export declare function preloadUMDBundles(defs: PluginDefinition[], baseUri?: string): void;
44
27
  export default class PluginLoader {
45
28
  definitions: PluginDefinition[];
46
29
  fetchESM?: (url: string) => Promise<LoadedPlugin>;
47
- fetchCJS?: (url: string) => Promise<LoadedPlugin>;
48
30
  constructor(defs?: PluginDefinition[], args?: {
49
31
  fetchESM?: (url: string) => Promise<LoadedPlugin>;
50
- fetchCJS?: (url: string) => Promise<LoadedPlugin>;
51
32
  });
52
- loadCJSPlugin(def: CJSPluginDefinition, baseUri?: string): Promise<LoadedPlugin>;
53
33
  loadESMPlugin(def: ESMPluginDefinition, baseUri?: string): Promise<LoadedPlugin>;
54
34
  loadUMDPlugin(def: UMDPluginDefinition | LegacyUMDPluginDefinition, baseUri?: string): Promise<{
55
35
  default: PluginConstructor;
56
36
  }>;
57
37
  loadPlugin(def: PluginDefinition, baseUri?: string): Promise<PluginConstructor>;
58
- installGlobalReExports(target: WindowOrWorkerGlobalScope): this;
59
- load(baseUri?: string): Promise<{
60
- plugin: PluginConstructor;
61
- definition: PluginDefinition;
62
- }[]>;
38
+ private reExports;
39
+ /**
40
+ * Ask for the runtime ABI (`JBrowseExports`) to be published on `target`
41
+ * before any plugin bundle is evaluated. Records the target and the loader;
42
+ * `loadSettled` fetches the registry, a ~126 KB gzipped module only a runtime
43
+ * plugin can use (see `ReExports/registry.ts` for why it cannot shrink).
44
+ *
45
+ * `registry` is the product's generated map — `reExports.generated.ts` on
46
+ * the main thread, `workerReExports.generated.ts` in its worker — which
47
+ * serves every `@jbrowse` package the product bundles. The caller names it
48
+ * because the registry serves this module: an `import()` of it from here is
49
+ * a cycle rolldown keeps in any host bundling this file, whether or not
50
+ * anything loads a plugin (EAGER_BUNDLE.md §3).
51
+ */
52
+ installGlobalReExports(target: WindowOrWorkerGlobalScope, registry: ReExportRegistryLoader): this;
53
+ private publishReExports;
54
+ /**
55
+ * Loads every definition and separates the ones that worked from the ones
56
+ * that didn't, instead of failing the batch on the first error.
57
+ *
58
+ * A remote config names its plugins at urls nobody re-checks — a store path
59
+ * that stops being republished, a bundle that needs a newer host than the one
60
+ * reading the config — and `load`'s all-or-nothing contract turns any of that
61
+ * into a dead app rather than a missing feature. That is the widest blast
62
+ * radius left in config loading: an unknown track/adapter/display type is
63
+ * already tolerated (the track is simply not usable), so the plugin url was
64
+ * the only field in a config that could still take a whole session down.
65
+ *
66
+ * Callers that can degrade (the apps) use this and report the failures;
67
+ * callers that cannot (the RPC worker, where a half-loaded plugin set would
68
+ * fail renders with a much worse message) keep using `load`.
69
+ */
70
+ loadSettled(baseUri?: string): Promise<{
71
+ records: PluginRecord[];
72
+ failures: PluginLoadFailure[];
73
+ }>;
74
+ load(baseUri?: string): Promise<PluginRecord[]>;
63
75
  }
64
- export {};
@@ -1,21 +1,50 @@
1
- import Plugin from "./Plugin.js";
2
- import ReExports from "./ReExports/index.js";
3
- import { isElectron } from "./util/index.js";
4
- export function isUMDPluginDefinition(def) {
5
- return ((def.umdUrl !== undefined ||
6
- def.url !== undefined ||
7
- def.umdLoc !== undefined) &&
8
- def.name !== undefined);
1
+ import { enableContractReports } from '@jbrowse/render-core/contractReports';
2
+ import { loudOnMissingModule, setReExportRegistry, } from './ReExports/registry.js';
3
+ import { isESMPluginDefinition, isUMDPluginDefinition, maybePluginUrl, pluginDescriptionString, pluginLabel, } from './pluginDefinitions.js';
4
+ import { isWebWorker } from './util/isWebWorker.js';
5
+ /**
6
+ * A definition names exactly one loader. More than one is malformed — no real
7
+ * config declares a plugin twice — and it is the shape that lets "the url we
8
+ * vetted" and "the url we run" drift apart, so refuse it rather than pick a
9
+ * winner. That keeps them the same string by construction, instead of by every
10
+ * url-based inspection of a definition remembering to match loadPlugin's order.
11
+ */
12
+ function assertSingleKind(def) {
13
+ const kinds = [
14
+ isESMPluginDefinition(def) ? 'ESM' : undefined,
15
+ isUMDPluginDefinition(def) ? 'UMD' : undefined,
16
+ ].filter(kind => kind !== undefined);
17
+ if (kinds.length > 1) {
18
+ throw new Error(`Plugin definition names more than one plugin type (${kinds.join(', ')}), refusing to load: ${JSON.stringify(def)}`);
19
+ }
9
20
  }
10
- export function isESMPluginDefinition(def) {
11
- return (def.esmUrl !== undefined ||
12
- def.esmLoc !== undefined);
21
+ /**
22
+ * A `cjsUrl` definition loaded by writing the bundle to a temp file and
23
+ * `require`ing it in Electron's renderer, the one loader that needed Node. That
24
+ * renderer runs UMD and ESM, and a plugin reaching the main process does it
25
+ * through `window.require('electron')` whatever format it ships in, so the
26
+ * format bought nothing its two peers do not. Name the successor rather than
27
+ * letting the definition fall through to "could not determine plugin type",
28
+ * which reads as a malformed config.
29
+ */
30
+ function assertRetiredKinds(def) {
31
+ if ('cjsUrl' in def) {
32
+ throw new Error(`CJS plugins are no longer loaded (${String(def.cjsUrl)}). Publish the plugin as UMD or ESM and name it with umdUrl or esmUrl.`);
33
+ }
13
34
  }
14
- function promisifiedLoadScript(src) {
35
+ function promisifiedLoadScript(src, integrity) {
15
36
  return new Promise((resolve, reject) => {
16
37
  const script = document.createElement('script');
17
38
  script.type = 'text/javascript';
18
39
  script.async = true;
40
+ // Subresource integrity guarantees the fetched bytes match the hash the
41
+ // plugin store published, so a tampered or swapped artifact fails to load.
42
+ // crossOrigin is required for the browser to enforce integrity on a
43
+ // cross-origin script.
44
+ if (integrity) {
45
+ script.integrity = integrity;
46
+ script.crossOrigin = 'anonymous';
47
+ }
19
48
  script.src = src;
20
49
  script.onload = () => {
21
50
  resolve(script.src);
@@ -26,111 +55,205 @@ function promisifiedLoadScript(src) {
26
55
  document.head.append(script);
27
56
  });
28
57
  }
29
- async function loadScript(scriptUrl) {
30
- if (!isInWebWorker()) {
31
- return promisifiedLoadScript(scriptUrl);
32
- }
33
- if (globalThis.importScripts) {
34
- await globalThis.importScripts(scriptUrl);
35
- return;
36
- }
37
- throw new Error('cannot figure out how to load external JS scripts in this environment');
58
+ function hasImportScripts(scope) {
59
+ return 'importScripts' in scope;
38
60
  }
39
- export function isCJSPluginDefinition(def) {
40
- return def.cjsUrl !== undefined;
61
+ // A *module* worker has importScripts on its global but throws from it — the
62
+ // spec forbids it there, and the browser says so ("Module scripts don't support
63
+ // importScripts"). That is the whole failure for a UMD plugin in a bundler
64
+ // configured for module workers (Vite's `worker.format: 'es'`), and it reads as
65
+ // a broken plugin unless named. Every other throw is the script's own — a 404,
66
+ // or a bundle that dereferences `window` in a realm that has none — and the
67
+ // script's words are the diagnosis, so they are kept rather than replaced.
68
+ export function workerScriptLoadMessage(scriptUrl, error) {
69
+ const detail = error instanceof Error ? error.message : String(error);
70
+ return /module script/i.test(detail)
71
+ ? `Failed to load ${scriptUrl} in the worker. A UMD plugin is loaded there via importScripts, which module workers do not support — either build the worker as a classic worker, or use a plugin published as ESM.`
72
+ : `Failed to load ${scriptUrl} in the worker: ${detail}`;
41
73
  }
42
- export function pluginDescriptionString(d) {
43
- if (isUMDPluginDefinition(d)) {
44
- return `UMD plugin ${d.name}`;
74
+ const workerPrefetches = new Map();
75
+ /**
76
+ * `importScripts` blocks until its file arrives, so a worker loading its
77
+ * plugins with it waited one round trip per plugin, in a row. Fetching them all
78
+ * first makes each `importScripts` a cache read — provided the fetch is the
79
+ * request `importScripts` makes: no-cors, with credentials. Chrome and Firefox
80
+ * both re-download for any other mode (probe-worker-script-cache.ts).
81
+ */
82
+ function prefetchWorkerScript(url) {
83
+ if (!workerPrefetches.has(url)) {
84
+ workerPrefetches.set(url, fetch(url, { mode: 'no-cors', credentials: 'include' })
85
+ .then(r => r.arrayBuffer())
86
+ .then(() => { }, () => { }));
45
87
  }
46
- else if (isESMPluginDefinition(d)) {
47
- return `ESM plugin ${d.esmUrl ||
48
- d.esmLoc.uri}`;
88
+ }
89
+ async function loadScript(scriptUrl, integrity) {
90
+ const scope = globalThis;
91
+ if (!isWebWorker()) {
92
+ return promisifiedLoadScript(scriptUrl, integrity);
49
93
  }
50
- else if (isCJSPluginDefinition(d)) {
51
- return `CJS plugin ${d.cjsUrl}`;
94
+ else if (hasImportScripts(scope)) {
95
+ await workerPrefetches.get(scriptUrl);
96
+ try {
97
+ scope.importScripts(scriptUrl);
98
+ }
99
+ catch (error) {
100
+ throw new Error(workerScriptLoadMessage(scriptUrl, error), {
101
+ cause: error,
102
+ });
103
+ }
104
+ return;
52
105
  }
53
106
  else {
54
- return 'unknown plugin';
107
+ throw new Error('cannot figure out how to load external JS scripts in this environment');
55
108
  }
56
109
  }
57
- export function pluginUrl(d) {
58
- if (isUMDPluginDefinition(d)) {
59
- return d.url ?? d.umdLoc?.uri ?? d.umdUrl;
110
+ /**
111
+ * Resolve a plugin's url, refusing anything that isn't http(s).
112
+ *
113
+ * `base` is the JBrowse **instance's** own location, not the config that named
114
+ * the plugin — every product passes `window.location.href` (the embedded ones
115
+ * let their host override it, the RPC worker forwards the same value). That is
116
+ * deliberate rather than an oversight: a relative url means "a plugin shipped
117
+ * beside this index.html". A config that means "beside *me*" has the
118
+ * `umdLoc`/`esmLoc` forms instead, which carry their own `baseUri` — the one
119
+ * `addRelativeUris` stamps from the config's url when it is fetched.
120
+ *
121
+ * The rule only bites on Desktop, whose instance is a `file://` page, so a
122
+ * relative url resolves to a `file:` url that could never be fetched. Diagnose
123
+ * that in terms its author can act on: the raw scheme of a url they never wrote
124
+ * ("Cannot load plugins using protocol file:") named the symptom and nothing
125
+ * else, and the reader is usually looking at a third-party hub config.
126
+ */
127
+ function resolvePluginUrl(spec, base) {
128
+ const url = new URL(spec, base);
129
+ if (url.protocol !== 'http:' && url.protocol !== 'https:') {
130
+ throw new Error(
131
+ // a spec with a scheme of its own resolved to exactly what it asked for,
132
+ // so there is nothing to explain beyond refusing it
133
+ /^[a-z][a-z0-9+.-]*:/i.test(spec)
134
+ ? `Cannot load plugins using protocol "${url.protocol}"`
135
+ : `Cannot load plugin from relative url "${spec}": it resolves against this JBrowse instance (${base}), not against the config that named it. Give it an absolute http(s) url, or use the umdLoc/esmLoc form to resolve it against the config.`);
60
136
  }
61
- else if (isESMPluginDefinition(d)) {
62
- return d.esmUrl ?? d.esmUri ?? d.esmLoc?.uri;
137
+ return url;
138
+ }
139
+ // A plugin served from the developer's own machine into an app built for
140
+ // production is the one arrangement that can only be a plugin under
141
+ // development: a shipped site serves its plugins from its own origin, and a
142
+ // developer running the app itself from source already has a development build.
143
+ // So it is the evidence that arms the contract channel without anything for the
144
+ // author to know about first — which is the whole difficulty the channel had,
145
+ // since the population it is written for is the one with nobody to ask. See
146
+ // `@jbrowse/render-core/contractReports`.
147
+ function armIfUnderDevelopment(def) {
148
+ const url = maybePluginUrl(def);
149
+ if (url !== undefined && servedFromThisMachine(url)) {
150
+ enableContractReports(`the plugin at ${url} is served from this machine`);
63
151
  }
64
- else if (isCJSPluginDefinition(d)) {
65
- return d.cjsUrl || d.cjsLoc.uri;
152
+ }
153
+ function servedFromThisMachine(url) {
154
+ try {
155
+ const { hostname, protocol } = new URL(url);
156
+ return ((protocol === 'http:' || protocol === 'https:') &&
157
+ (hostname === 'localhost' ||
158
+ hostname === '127.0.0.1' ||
159
+ hostname === '[::1]'));
66
160
  }
67
- else {
68
- return 'unknown url';
161
+ catch {
162
+ // a relative url is a plugin shipped beside this index.html, which is the
163
+ // site's own rather than one under development
164
+ return false;
69
165
  }
70
166
  }
71
- function isInWebWorker() {
72
- return 'WorkerGlobalScope' in globalThis;
73
- }
74
167
  function addCacheBuster(url) {
75
- if (!globalThis.__jbrowseCacheBuster) {
168
+ if (!('__jbrowseCacheBuster' in globalThis)) {
76
169
  return url;
77
170
  }
78
171
  const u = new URL(url);
79
172
  u.searchParams.set('_cb', Date.now().toString());
80
173
  return u.href;
81
174
  }
175
+ function umdPluginUrl(def, baseUri) {
176
+ return 'url' in def
177
+ ? resolvePluginUrl(def.url, baseUri)
178
+ : 'umdUrl' in def
179
+ ? resolvePluginUrl(def.umdUrl, baseUri)
180
+ : resolvePluginUrl(def.umdLoc.uri, def.umdLoc.baseUri);
181
+ }
182
+ /**
183
+ * The registry has to be published before a plugin bundle runs, but not before
184
+ * it downloads, so each bundle is preloaded while the registry is fetched.
185
+ * Skipped under the cache-buster, whose query string differs per request.
186
+ *
187
+ * Exported for a worker told its plugins ahead of its boot configuration.
188
+ */
189
+ export function preloadUMDBundles(defs, baseUri) {
190
+ if ('__jbrowseCacheBuster' in globalThis) {
191
+ return;
192
+ }
193
+ if (isWebWorker()) {
194
+ for (const def of defs) {
195
+ if (isUMDPluginDefinition(def)) {
196
+ try {
197
+ prefetchWorkerScript(umdPluginUrl(def, baseUri).href);
198
+ }
199
+ catch {
200
+ // loadPlugin reports a url it cannot resolve
201
+ }
202
+ }
203
+ }
204
+ return;
205
+ }
206
+ if (typeof document === 'undefined') {
207
+ return;
208
+ }
209
+ for (const def of defs) {
210
+ if (isUMDPluginDefinition(def)) {
211
+ try {
212
+ const link = document.createElement('link');
213
+ link.rel = 'preload';
214
+ link.as = 'script';
215
+ if (def.integrity) {
216
+ link.setAttribute('integrity', def.integrity);
217
+ link.setAttribute('crossorigin', 'anonymous');
218
+ }
219
+ link.href = umdPluginUrl(def, baseUri).href;
220
+ document.head.append(link);
221
+ }
222
+ catch {
223
+ // loadPlugin reports a url it cannot resolve
224
+ }
225
+ }
226
+ }
227
+ }
82
228
  export default class PluginLoader {
83
229
  definitions = [];
84
230
  fetchESM;
85
- fetchCJS;
86
231
  constructor(defs = [], args) {
87
232
  this.fetchESM = args?.fetchESM;
88
- this.fetchCJS = args?.fetchCJS;
89
- this.definitions = JSON.parse(JSON.stringify(defs));
90
- }
91
- async loadCJSPlugin(def, baseUri) {
92
- const parsedUrl = new URL(def.cjsUrl, baseUri);
93
- if (parsedUrl.protocol !== 'http:' && parsedUrl.protocol !== 'https:') {
94
- throw new Error(`Cannot load plugins using protocol "${parsedUrl.protocol}"`);
95
- }
96
- if (!this.fetchCJS) {
97
- throw new Error('No fetchCJS callback provided');
98
- }
99
- return this.fetchCJS(parsedUrl.href);
233
+ this.definitions = structuredClone(defs);
100
234
  }
101
235
  async loadESMPlugin(def, baseUri) {
102
236
  const parsedUrl = 'esmUrl' in def
103
- ? new URL(def.esmUrl, baseUri)
104
- : new URL(def.esmLoc.uri, def.esmLoc.baseUri);
105
- if (parsedUrl.protocol !== 'http:' && parsedUrl.protocol !== 'https:') {
106
- throw new Error(`cannot load plugins using protocol "${parsedUrl.protocol}"`);
107
- }
237
+ ? resolvePluginUrl(def.esmUrl, baseUri)
238
+ : resolvePluginUrl(def.esmLoc.uri, def.esmLoc.baseUri);
108
239
  if (!this.fetchESM) {
109
240
  throw new Error('No ESM fetcher installed');
110
241
  }
111
242
  const plugin = await this.fetchESM(addCacheBuster(parsedUrl.href));
243
+ // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
112
244
  if (!plugin) {
113
245
  throw new Error(`Could not load ESM plugin: ${parsedUrl}`);
114
246
  }
115
247
  return plugin;
116
248
  }
117
249
  async loadUMDPlugin(def, baseUri) {
118
- const parsedUrl = 'url' in def
119
- ? new URL(def.url, baseUri)
120
- : 'umdUrl' in def
121
- ? new URL(def.umdUrl, baseUri)
122
- : new URL(def.umdLoc.uri, def.umdLoc.baseUri);
123
- if (parsedUrl.protocol !== 'http:' && parsedUrl.protocol !== 'https:') {
124
- throw new Error(`cannot load plugins using protocol "${parsedUrl.protocol}"`);
125
- }
250
+ const parsedUrl = umdPluginUrl(def, baseUri);
126
251
  const moduleName = def.name;
127
252
  const umdName = `JBrowsePlugin${moduleName}`;
128
- if (typeof jest === 'undefined') {
129
- await loadScript(addCacheBuster(parsedUrl.href));
130
- }
131
- else {
132
- globalThis[umdName] = { default: Plugin };
133
- }
253
+ // a cache buster query string would change the bytes the browser hashes for
254
+ // SRI, so skip it when an integrity hash is present (the url is already
255
+ // version-pinned and immutable, so cache-busting is unnecessary anyway)
256
+ await loadScript(def.integrity ? parsedUrl.href : addCacheBuster(parsedUrl.href), def.integrity);
134
257
  const plugin = globalThis[umdName];
135
258
  if (!plugin) {
136
259
  throw new Error(`Failed to load UMD bundle for ${moduleName}, ${umdName} is undefined`);
@@ -138,37 +261,114 @@ export default class PluginLoader {
138
261
  return plugin;
139
262
  }
140
263
  async loadPlugin(def, baseUri) {
264
+ assertRetiredKinds(def);
265
+ assertSingleKind(def);
266
+ armIfUnderDevelopment(def);
141
267
  let plugin;
142
- if (isElectron && isCJSPluginDefinition(def)) {
143
- plugin = await this.loadCJSPlugin(def, baseUri);
144
- }
145
- else if (isESMPluginDefinition(def)) {
268
+ if (isESMPluginDefinition(def)) {
146
269
  plugin = await this.loadESMPlugin(def, baseUri);
147
270
  }
148
271
  else if (isUMDPluginDefinition(def)) {
149
272
  plugin = await this.loadUMDPlugin(def, baseUri);
150
273
  }
151
- else if (!isElectron && isCJSPluginDefinition(def)) {
152
- throw new Error(`CommonJS plugin found, but not in a NodeJS environment: ${JSON.stringify(def)}`);
153
- }
154
274
  else {
155
275
  throw new Error(`Could not determine plugin type: ${JSON.stringify(def)}`);
156
276
  }
277
+ // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
157
278
  if (!plugin.default) {
158
279
  throw new Error(`${pluginDescriptionString(def)} does not have a default export, cannot load`);
159
280
  }
160
281
  return plugin.default;
161
282
  }
162
- installGlobalReExports(target) {
163
- target.JBrowseExports = Object.fromEntries(Object.entries(ReExports).map(([moduleName, module]) => {
164
- return [moduleName, module];
165
- }));
283
+ reExports;
284
+ /**
285
+ * Ask for the runtime ABI (`JBrowseExports`) to be published on `target`
286
+ * before any plugin bundle is evaluated. Records the target and the loader;
287
+ * `loadSettled` fetches the registry, a ~126 KB gzipped module only a runtime
288
+ * plugin can use (see `ReExports/registry.ts` for why it cannot shrink).
289
+ *
290
+ * `registry` is the product's generated map — `reExports.generated.ts` on
291
+ * the main thread, `workerReExports.generated.ts` in its worker — which
292
+ * serves every `@jbrowse` package the product bundles. The caller names it
293
+ * because the registry serves this module: an `import()` of it from here is
294
+ * a cycle rolldown keeps in any host bundling this file, whether or not
295
+ * anything loads a plugin (EAGER_BUNDLE.md §3).
296
+ */
297
+ installGlobalReExports(target, registry) {
298
+ this.reExports = { target, registry };
166
299
  return this;
167
300
  }
168
- async load(baseUri) {
169
- return Promise.all(this.definitions.map(async (definition) => ({
301
+ async publishReExports() {
302
+ if (!this.reExports) {
303
+ return;
304
+ }
305
+ const { target, registry } = this.reExports;
306
+ const { default: ReExports } = await registry();
307
+ target.JBrowseExports =
308
+ loudOnMissingModule({ ...ReExports });
309
+ // the synchronous half: `pluginManager.jbrequire(name)` is what a CJS
310
+ // plugin calls, and it cannot await
311
+ setReExportRegistry(ReExports);
312
+ this.reExports = undefined;
313
+ }
314
+ /**
315
+ * Loads every definition and separates the ones that worked from the ones
316
+ * that didn't, instead of failing the batch on the first error.
317
+ *
318
+ * A remote config names its plugins at urls nobody re-checks — a store path
319
+ * that stops being republished, a bundle that needs a newer host than the one
320
+ * reading the config — and `load`'s all-or-nothing contract turns any of that
321
+ * into a dead app rather than a missing feature. That is the widest blast
322
+ * radius left in config loading: an unknown track/adapter/display type is
323
+ * already tolerated (the track is simply not usable), so the plugin url was
324
+ * the only field in a config that could still take a whole session down.
325
+ *
326
+ * Callers that can degrade (the apps) use this and report the failures;
327
+ * callers that cannot (the RPC worker, where a half-loaded plugin set would
328
+ * fail renders with a much worse message) keep using `load`.
329
+ */
330
+ async loadSettled(baseUri) {
331
+ preloadUMDBundles(this.definitions, baseUri);
332
+ // before the first plugin script evaluates — a UMD bundle reads
333
+ // `JBrowseExports` off the global at module scope
334
+ await this.publishReExports();
335
+ const results = await Promise.allSettled(this.definitions.map(async (definition) => ({
170
336
  plugin: await this.loadPlugin(definition, baseUri),
171
337
  definition,
172
338
  })));
339
+ const records = [];
340
+ const failures = [];
341
+ for (const [i, result] of results.entries()) {
342
+ if (result.status === 'fulfilled') {
343
+ records.push(result.value);
344
+ }
345
+ else {
346
+ failures.push({
347
+ definition: this.definitions[i],
348
+ error: result.reason,
349
+ });
350
+ }
351
+ }
352
+ return { records, failures };
353
+ }
354
+ async load(baseUri) {
355
+ const { records, failures } = await this.loadSettled(baseUri);
356
+ // rethrown by definition order rather than by which rejected first, so the
357
+ // error a strict caller sees doesn't depend on network timing.
358
+ //
359
+ // Named, because the RPC worker calls this: a plugin that throws while
360
+ // evaluating takes the whole RpcServer with it, and the bare error is
361
+ // whatever the bundle's module scope said — `Cannot read properties of
362
+ // undefined`, or the missing ABI key — with nothing saying which plugin
363
+ // read it. The message is carried rather than the error, since this one
364
+ // crosses postMessage and `serializeError` cannot clone an arbitrary
365
+ // `cause`.
366
+ const failure = failures[0];
367
+ if (failure) {
368
+ const { definition, error } = failure;
369
+ const detail = error instanceof Error ? error.message : String(error);
370
+ throw new Error(`plugin ${pluginLabel(definition)} failed: ${detail}`);
371
+ }
372
+ return records;
173
373
  }
174
374
  }