@jbrowse/core 1.7.11 → 2.1.0

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 (204) hide show
  1. package/BaseFeatureWidget/BaseFeatureDetail.d.ts +20 -4
  2. package/BaseFeatureWidget/BaseFeatureDetail.js +313 -558
  3. package/BaseFeatureWidget/SequenceFeatureDetails.js +213 -473
  4. package/BaseFeatureWidget/index.d.ts +2 -2
  5. package/BaseFeatureWidget/index.js +88 -124
  6. package/BaseFeatureWidget/types.d.ts +1 -0
  7. package/BaseFeatureWidget/types.js +1 -4
  8. package/BaseFeatureWidget/util.js +40 -75
  9. package/CorePlugin.js +55 -94
  10. package/Plugin.js +9 -34
  11. package/PluginLoader.js +153 -422
  12. package/PluginManager.d.ts +84 -117
  13. package/PluginManager.js +377 -666
  14. package/ReExports/Attributes.d.ts +2 -0
  15. package/ReExports/Attributes.js +5 -0
  16. package/ReExports/BaseCard.d.ts +2 -0
  17. package/ReExports/BaseCard.js +5 -0
  18. package/ReExports/DataGrid.d.ts +2 -0
  19. package/ReExports/DataGrid.js +6 -0
  20. package/ReExports/FeatureDetails.d.ts +2 -0
  21. package/ReExports/FeatureDetails.js +5 -0
  22. package/ReExports/index.js +6 -12
  23. package/ReExports/list.d.ts +5 -0
  24. package/ReExports/list.js +271 -7
  25. package/ReExports/material-ui-colors.d.ts +1 -19
  26. package/ReExports/material-ui-colors.js +16 -158
  27. package/ReExports/modules.d.ts +68 -109
  28. package/ReExports/modules.js +455 -244
  29. package/TextSearch/BaseResults.js +51 -123
  30. package/TextSearch/TextSearchManager.d.ts +3 -1
  31. package/TextSearch/TextSearchManager.js +66 -144
  32. package/assemblyManager/assembly.js +280 -554
  33. package/assemblyManager/assemblyConfigSchema.js +47 -64
  34. package/assemblyManager/assemblyManager.d.ts +12 -10
  35. package/assemblyManager/assemblyManager.js +126 -270
  36. package/assemblyManager/index.js +9 -22
  37. package/configuration/configurationSchema.js +167 -203
  38. package/configuration/configurationSlot.js +248 -326
  39. package/configuration/index.js +19 -35
  40. package/configuration/util.d.ts +1 -1
  41. package/configuration/util.js +131 -173
  42. package/data_adapters/BaseAdapter.d.ts +2 -2
  43. package/data_adapters/BaseAdapter.js +132 -521
  44. package/data_adapters/CytobandAdapter.js +40 -126
  45. package/data_adapters/dataAdapterCache.js +77 -158
  46. package/package.json +16 -18
  47. package/pluggableElementTypes/AdapterType.js +24 -79
  48. package/pluggableElementTypes/AddTrackWorkflowType.d.ts +17 -0
  49. package/pluggableElementTypes/AddTrackWorkflowType.js +20 -0
  50. package/pluggableElementTypes/ConnectionType.js +22 -65
  51. package/pluggableElementTypes/DisplayType.js +35 -82
  52. package/pluggableElementTypes/InternetAccountType.js +23 -64
  53. package/pluggableElementTypes/PluggableElementBase.js +8 -20
  54. package/pluggableElementTypes/RpcMethodType.js +85 -427
  55. package/pluggableElementTypes/TextSearchAdapterType.js +16 -55
  56. package/pluggableElementTypes/TrackType.js +26 -70
  57. package/pluggableElementTypes/ViewType.js +21 -63
  58. package/pluggableElementTypes/WidgetType.js +21 -64
  59. package/pluggableElementTypes/index.d.ts +4 -3
  60. package/pluggableElementTypes/index.js +42 -125
  61. package/pluggableElementTypes/models/BaseConnectionModelFactory.js +28 -43
  62. package/pluggableElementTypes/models/BaseDisplayModel.d.ts +10 -10
  63. package/pluggableElementTypes/models/BaseDisplayModel.js +58 -95
  64. package/pluggableElementTypes/models/BaseTrackModel.d.ts +1 -1
  65. package/pluggableElementTypes/models/BaseTrackModel.js +139 -200
  66. package/pluggableElementTypes/models/BaseViewModel.js +24 -40
  67. package/pluggableElementTypes/models/InternetAccountModel.js +116 -263
  68. package/pluggableElementTypes/models/baseConnectionConfig.js +14 -25
  69. package/pluggableElementTypes/models/baseInternetAccountConfig.js +29 -38
  70. package/pluggableElementTypes/models/baseTrackConfig.js +106 -133
  71. package/pluggableElementTypes/models/index.js +21 -70
  72. package/pluggableElementTypes/renderers/BoxRendererType.js +132 -291
  73. package/pluggableElementTypes/renderers/CircularChordRendererType.js +8 -38
  74. package/pluggableElementTypes/renderers/ComparativeServerSideRendererType.js +60 -192
  75. package/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -2
  76. package/pluggableElementTypes/renderers/FeatureRendererType.js +89 -255
  77. package/pluggableElementTypes/renderers/RendererType.js +31 -105
  78. package/pluggableElementTypes/renderers/ServerSideRenderedContent.js +61 -72
  79. package/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +2 -2
  80. package/pluggableElementTypes/renderers/ServerSideRendererType.js +112 -265
  81. package/pluggableElementTypes/renderers/index.js +19 -62
  82. package/pluggableElementTypes/renderers/util/serializableFilterChain.js +27 -65
  83. package/rpc/BaseRpcDriver.js +169 -405
  84. package/rpc/MainThreadRpcDriver.js +27 -150
  85. package/rpc/RpcManager.js +58 -159
  86. package/rpc/WebWorkerRpcDriver.js +54 -171
  87. package/rpc/configSchema.js +25 -49
  88. package/rpc/coreRpcMethods.d.ts +1 -3
  89. package/rpc/coreRpcMethods.js +221 -959
  90. package/rpc/remoteAbortSignals.js +46 -70
  91. package/tsconfig.build.tsbuildinfo +1 -1
  92. package/ui/AboutDialog.js +107 -158
  93. package/ui/App.js +157 -261
  94. package/ui/AssemblySelector.d.ts +1 -1
  95. package/ui/AssemblySelector.js +59 -115
  96. package/ui/CascadingMenu.js +100 -199
  97. package/ui/ColorPicker.d.ts +16 -0
  98. package/ui/ColorPicker.js +97 -0
  99. package/ui/Drawer.js +28 -58
  100. package/ui/DrawerWidget.js +109 -209
  101. package/ui/DropDownMenu.d.ts +0 -8
  102. package/ui/DropDownMenu.js +60 -97
  103. package/ui/EditableTypography.d.ts +1 -1
  104. package/ui/EditableTypography.js +87 -155
  105. package/ui/ErrorMessage.js +41 -66
  106. package/ui/FactoryResetDialog.js +24 -57
  107. package/ui/FatalErrorDialog.js +59 -91
  108. package/ui/FileSelector/FileSelector.js +123 -189
  109. package/ui/FileSelector/LocalFileChooser.js +44 -71
  110. package/ui/FileSelector/UrlChooser.js +17 -38
  111. package/ui/FileSelector/index.js +6 -12
  112. package/ui/Icons.d.ts +1 -1
  113. package/ui/Icons.js +45 -69
  114. package/ui/Logo.js +57 -110
  115. package/ui/Menu.d.ts +1 -1
  116. package/ui/Menu.js +232 -355
  117. package/ui/PrerenderedCanvas.js +63 -78
  118. package/ui/ResizeHandle.js +87 -114
  119. package/ui/ReturnToImportFormDialog.js +32 -59
  120. package/ui/SanitizedHTML.js +63 -52
  121. package/ui/Snackbar.js +74 -99
  122. package/ui/SnackbarModel.js +37 -51
  123. package/ui/Tooltip.d.ts +3 -1
  124. package/ui/Tooltip.js +49 -74
  125. package/ui/ViewContainer.js +113 -183
  126. package/ui/colors.d.ts +10 -0
  127. package/ui/colors.js +78 -0
  128. package/ui/index.js +51 -181
  129. package/ui/react-colorful.d.ts +17 -0
  130. package/ui/react-colorful.js +455 -0
  131. package/ui/theme.d.ts +279 -131
  132. package/ui/theme.js +197 -225
  133. package/util/Base1DUtils.d.ts +32 -0
  134. package/util/Base1DUtils.js +174 -0
  135. package/util/Base1DViewModel.d.ts +16 -37
  136. package/util/Base1DViewModel.js +116 -295
  137. package/util/QuickLRU.js +84 -332
  138. package/util/TimeTraveller.d.ts +19 -0
  139. package/util/TimeTraveller.js +86 -0
  140. package/util/aborting.js +49 -127
  141. package/util/analytics.js +91 -154
  142. package/util/blockTypes.js +106 -240
  143. package/util/calculateDynamicBlocks.js +98 -128
  144. package/util/calculateStaticBlocks.js +105 -125
  145. package/util/color/cssColorsLevel4.js +156 -160
  146. package/util/color/index.js +33 -55
  147. package/util/compositeMap.js +49 -333
  148. package/util/formatFastaStrings.js +9 -14
  149. package/util/idMaker.js +18 -31
  150. package/util/index.d.ts +18 -39
  151. package/util/index.js +743 -1236
  152. package/util/io/RemoteFileWithRangeCache.js +88 -257
  153. package/util/io/index.js +95 -169
  154. package/util/jexl.js +60 -115
  155. package/util/jexlStrings.js +24 -29
  156. package/util/layouts/BaseLayout.js +1 -4
  157. package/util/layouts/GranularRectLayout.js +388 -557
  158. package/util/layouts/MultiLayout.js +41 -109
  159. package/util/layouts/PrecomputedLayout.js +56 -114
  160. package/util/layouts/PrecomputedMultiLayout.js +22 -59
  161. package/util/layouts/SceneGraph.js +127 -197
  162. package/util/layouts/index.js +29 -66
  163. package/util/mst-reflection.js +55 -71
  164. package/util/offscreenCanvasPonyfill.js +66 -134
  165. package/util/offscreenCanvasUtils.d.ts +2 -7
  166. package/util/offscreenCanvasUtils.js +49 -146
  167. package/util/range.js +29 -40
  168. package/util/rxjs.js +20 -27
  169. package/util/simpleFeature.js +88 -152
  170. package/util/stats.js +91 -151
  171. package/util/tracks.js +130 -171
  172. package/util/types/index.d.ts +3 -3
  173. package/util/types/index.js +110 -179
  174. package/util/types/mst.d.ts +3 -3
  175. package/util/types/mst.js +91 -142
  176. package/util/types/util.js +1 -4
  177. package/util/when.js +54 -101
  178. package/BaseFeatureWidget/SequenceFeatureDetails.test.js +0 -122
  179. package/BaseFeatureWidget/index.test.js +0 -51
  180. package/TextSearch/BaseResults.test.js +0 -42
  181. package/configuration/configurationSchema.test.js +0 -266
  182. package/configuration/configurationSlot.test.js +0 -69
  183. package/configuration/util.test.js +0 -39
  184. package/data_adapters/BaseAdapter.test.js +0 -200
  185. package/declare.d.js +0 -1
  186. package/pluggableElementTypes/RpcMethodType.test.js +0 -118
  187. package/pluggableElementTypes/renderers/declare.d.js +0 -1
  188. package/pluggableElementTypes/renderers/util/serializableFilterChain.test.js +0 -20
  189. package/rpc/BaseRpcDriver.test.js +0 -540
  190. package/rpc/declaration.d.js +0 -1
  191. package/ui/FatalErrorDialog.test.js +0 -82
  192. package/ui/SanitizedHTML.test.js +0 -36
  193. package/ui/theme.test.js +0 -111
  194. package/util/Base1DViewModel.test.js +0 -130
  195. package/util/calculateDynamicBlocks.test.js +0 -74
  196. package/util/calculateStaticBlocks.test.js +0 -297
  197. package/util/declare.d.js +0 -1
  198. package/util/formatFastaStrings.test.js +0 -40
  199. package/util/index.test.js +0 -213
  200. package/util/jexlStrings.test.js +0 -48
  201. package/util/layouts/GranularRectLayout.test.js +0 -99
  202. package/util/range.test.js +0 -64
  203. package/util/simpleFeature.test.js +0 -34
  204. package/util/stats.test.js +0 -172
@@ -1,128 +1,42 @@
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  "use strict";
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-
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- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
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-
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- Object.defineProperty(exports, "__esModule", {
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- value: true
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- });
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- exports.configSchema = exports.DataAdapter = void 0;
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-
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- var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
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-
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- var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
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-
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- var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
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-
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- var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
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-
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- var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
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-
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- var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
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-
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- var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
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-
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- var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
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-
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- var _simpleFeature = _interopRequireDefault(require("../util/simpleFeature"));
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-
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- var _configuration = require("../configuration");
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-
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- var _io = require("../util/io");
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-
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- var _BaseAdapter2 = require("./BaseAdapter");
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-
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- function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
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-
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- function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
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-
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- var configSchema = (0, _configuration.ConfigurationSchema)('CytobandAdapter', {
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- cytobandLocation: {
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- type: 'fileLocation',
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- defaultValue: {
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- uri: '/path/to/cytoband.txt.gz'
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- }
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- }
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- }, {
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- explicitlyTyped: true
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- });
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+ var __importDefault = (this && this.__importDefault) || function (mod) {
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+ return (mod && mod.__esModule) ? mod : { "default": mod };
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+ };
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+ Object.defineProperty(exports, "__esModule", { value: true });
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+ exports.DataAdapter = exports.configSchema = void 0;
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+ const simpleFeature_1 = __importDefault(require("../util/simpleFeature"));
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+ const configuration_1 = require("../configuration");
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+ const io_1 = require("../util/io");
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+ const BaseAdapter_1 = require("./BaseAdapter");
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+ const configSchema = (0, configuration_1.ConfigurationSchema)('CytobandAdapter', {
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+ cytobandLocation: {
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+ type: 'fileLocation',
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+ defaultValue: { uri: '/path/to/cytoband.txt.gz' },
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+ },
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+ }, { explicitlyTyped: true });
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  exports.configSchema = configSchema;
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-
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- var CytobandAdapter = /*#__PURE__*/function (_BaseAdapter) {
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- (0, _inherits2.default)(CytobandAdapter, _BaseAdapter);
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-
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- var _super = _createSuper(CytobandAdapter);
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-
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- function CytobandAdapter() {
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- (0, _classCallCheck2.default)(this, CytobandAdapter);
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- return _super.apply(this, arguments);
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- }
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-
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- (0, _createClass2.default)(CytobandAdapter, [{
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- key: "getData",
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- value: function () {
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- var _getData = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
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- var loc, data;
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- return _regenerator.default.wrap(function _callee$(_context) {
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- while (1) {
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- switch (_context.prev = _context.next) {
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- case 0:
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- loc = (0, _configuration.readConfObject)(this.config, 'cytobandLocation');
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-
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- if (!(loc.uri === '' || loc.uri === '/path/to/cytoband.txt.gz')) {
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- _context.next = 3;
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- break;
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- }
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-
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- return _context.abrupt("return", []);
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-
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- case 3:
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- _context.next = 5;
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- return (0, _io.openLocation)(loc).readFile('utf8');
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-
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- case 5:
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- data = _context.sent;
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- return _context.abrupt("return", data.split('\n').filter(function (f) {
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- return !!f.trim();
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- }).map(function (line) {
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- var _line$split = line.split('\t'),
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- _line$split2 = (0, _slicedToArray2.default)(_line$split, 5),
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- refName = _line$split2[0],
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- start = _line$split2[1],
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- end = _line$split2[2],
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- name = _line$split2[3],
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- type = _line$split2[4];
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-
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- return new _simpleFeature.default({
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- uniqueId: line,
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- refName: refName,
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- start: +start,
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- end: +end,
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- name: name,
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- type: type
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- });
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- }));
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-
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- case 7:
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- case "end":
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- return _context.stop();
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- }
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- }
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- }, _callee, this);
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- }));
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-
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- function getData() {
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- return _getData.apply(this, arguments);
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- }
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-
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- return getData;
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- }()
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- }, {
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- key: "freeResources",
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- value: function
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- /* { region } */
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- freeResources() {}
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- }]);
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- return CytobandAdapter;
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- }(_BaseAdapter2.BaseAdapter);
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-
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- exports.DataAdapter = CytobandAdapter;
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+ class CytobandAdapter extends BaseAdapter_1.BaseAdapter {
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+ async getData() {
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+ const loc = (0, configuration_1.readConfObject)(this.config, 'cytobandLocation');
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+ if (loc.uri === '' || loc.uri === '/path/to/cytoband.txt.gz') {
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+ return [];
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+ }
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+ const data = await (0, io_1.openLocation)(loc).readFile('utf8');
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+ return data
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+ .split('\n')
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+ .filter(f => !!f.trim())
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+ .map(line => {
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+ const [refName, start, end, name, type] = line.split('\t');
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+ return new simpleFeature_1.default({
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+ uniqueId: line,
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+ refName,
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+ start: +start,
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+ end: +end,
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+ name,
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+ type,
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+ });
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+ });
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+ }
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+ freeResources( /* { region } */) { }
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+ }
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+ exports.DataAdapter = CytobandAdapter;
@@ -1,27 +1,14 @@
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  "use strict";
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-
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- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
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-
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- Object.defineProperty(exports, "__esModule", {
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- value: true
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- });
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- exports.clearAdapterCache = clearAdapterCache;
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- exports.freeAdapterResources = freeAdapterResources;
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- exports.getAdapter = getAdapter;
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-
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- var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
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-
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- var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
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-
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- var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
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-
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- var _idMaker = _interopRequireDefault(require("../util/idMaker"));
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-
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+ var __importDefault = (this && this.__importDefault) || function (mod) {
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+ return (mod && mod.__esModule) ? mod : { "default": mod };
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+ };
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+ Object.defineProperty(exports, "__esModule", { value: true });
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+ exports.clearAdapterCache = exports.freeAdapterResources = exports.getAdapter = void 0;
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+ const idMaker_1 = __importDefault(require("../util/idMaker"));
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  function adapterConfigCacheKey(adapterConfig) {
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- return "".concat((0, _idMaker.default)(adapterConfig));
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+ return `${(0, idMaker_1.default)(adapterConfig)}`;
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  }
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-
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- var adapterCache = {};
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+ let adapterCache = {};
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  /**
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  * instantiate a data adapter, or return an already-instantiated one if we have one with the same
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  * configuration
@@ -31,149 +18,81 @@ var adapterCache = {};
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  * used for reference counting
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  * @param adapterConfigSnapshot - plain-JS configuration snapshot for the adapter
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-
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- function getAdapter(_x, _x2, _x3) {
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- return _getAdapter.apply(this, arguments);
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- }
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- /**
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- * this is a callback that is passed to adapters that
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- * allows them to get any sub-adapters that they need
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- * internally, staying with the same worker session ID
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- */
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-
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-
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- function _getAdapter() {
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- _getAdapter = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(pluginManager, sessionId, adapterConfigSnapshot) {
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- var cacheKey, adapterType, dataAdapterType, adapterConfig, getSubAdapter, AdapterClass, getAdapterClass, CLASS, dataAdapter, cacheEntry;
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- return _regenerator.default.wrap(function _callee$(_context) {
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- while (1) {
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- switch (_context.prev = _context.next) {
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- case 0:
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- // cache the adapter object
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- cacheKey = adapterConfigCacheKey(adapterConfigSnapshot);
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-
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- if (adapterCache[cacheKey]) {
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- _context.next = 21;
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- break;
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- }
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-
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- adapterType = (adapterConfigSnapshot || {}).type;
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-
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- if (adapterType) {
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- _context.next = 5;
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- break;
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- }
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-
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+ async function getAdapter(pluginManager, sessionId, adapterConfigSnapshot) {
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+ // cache the adapter object
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+ const cacheKey = adapterConfigCacheKey(adapterConfigSnapshot);
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+ if (!adapterCache[cacheKey]) {
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+ const adapterType = (adapterConfigSnapshot || {}).type;
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+ if (!adapterType) {
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  throw new Error('could not determine adapter type from adapter config snapshot');
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-
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- case 5:
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- dataAdapterType = pluginManager.getAdapterType(adapterType);
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-
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- if (dataAdapterType) {
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- _context.next = 8;
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- break;
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- }
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-
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- throw new Error("unknown data adapter type ".concat(adapterType));
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-
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- case 8:
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- // instantiate the data adapter's config schema so it gets its defaults,
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- // callbacks, etc
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- adapterConfig = dataAdapterType.configSchema.create(adapterConfigSnapshot, {
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- pluginManager: pluginManager
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- });
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- getSubAdapter = getAdapter.bind(null, pluginManager, sessionId); // instantiate the adapter itself with its config schema, and a bound
86
- // func that it can use to get any inner adapters
87
- // (such as sequence adapters or wrapped subadapters) that it needs
88
- //
89
-
90
- AdapterClass = dataAdapterType.AdapterClass, getAdapterClass = dataAdapterType.getAdapterClass; // @ts-ignore
91
-
92
- _context.t0 = AdapterClass;
93
-
94
- if (_context.t0) {
95
- _context.next = 16;
96
- break;
97
- }
98
-
99
- _context.next = 15;
100
- return getAdapterClass();
101
-
102
- case 15:
103
- _context.t0 = _context.sent;
104
-
105
- case 16:
106
- CLASS = _context.t0;
107
-
108
- if (CLASS) {
109
- _context.next = 19;
110
- break;
111
- }
112
-
28
+ }
29
+ const dataAdapterType = pluginManager.getAdapterType(adapterType);
30
+ if (!dataAdapterType) {
31
+ throw new Error(`unknown data adapter type ${adapterType}`);
32
+ }
33
+ // instantiate the data adapter's config schema so it gets its defaults,
34
+ // callbacks, etc
35
+ const adapterConfig = dataAdapterType.configSchema.create(adapterConfigSnapshot, { pluginManager });
36
+ const getSubAdapter = getAdapter.bind(null, pluginManager, sessionId);
37
+ // instantiate the adapter itself with its config schema, and a bound
38
+ // func that it can use to get any inner adapters
39
+ // (such as sequence adapters or wrapped subadapters) that it needs
40
+ //
41
+ const { AdapterClass, getAdapterClass } = dataAdapterType;
42
+ // @ts-ignore
43
+ const CLASS = AdapterClass || (await getAdapterClass());
44
+ if (!CLASS) {
113
45
  throw new Error('Failed to get adapter');
114
-
115
- case 19:
116
- dataAdapter = new CLASS(adapterConfig, getSubAdapter, pluginManager); // store it in our cache
117
-
118
- adapterCache[cacheKey] = {
119
- dataAdapter: dataAdapter,
120
- sessionIds: new Set([sessionId])
121
- };
122
-
123
- case 21:
124
- cacheEntry = adapterCache[cacheKey];
125
- cacheEntry.sessionIds.add(sessionId);
126
- return _context.abrupt("return", cacheEntry);
127
-
128
- case 24:
129
- case "end":
130
- return _context.stop();
131
46
  }
132
- }
133
- }, _callee);
134
- }));
135
- return _getAdapter.apply(this, arguments);
47
+ const dataAdapter = new CLASS(adapterConfig, getSubAdapter, pluginManager);
48
+ // store it in our cache
49
+ adapterCache[cacheKey] = {
50
+ dataAdapter,
51
+ sessionIds: new Set([sessionId]),
52
+ };
53
+ }
54
+ const cacheEntry = adapterCache[cacheKey];
55
+ cacheEntry.sessionIds.add(sessionId);
56
+ return cacheEntry;
136
57
  }
137
-
58
+ exports.getAdapter = getAdapter;
138
59
  // eslint-disable-next-line @typescript-eslint/no-explicit-any
139
60
  function freeAdapterResources(specification) {
140
- var deleteCount = 0;
141
- var specKeys = Object.keys(specification); // if we don't specify a range, delete any adapters that are
142
- // only associated with that session
143
-
144
- if (specKeys.length === 1 && specKeys[0] === 'sessionId') {
145
- var sessionId = specification.sessionId;
146
- Object.entries(adapterCache).forEach(function (_ref) {
147
- var _ref2 = (0, _slicedToArray2.default)(_ref, 2),
148
- cacheKey = _ref2[0],
149
- cacheEntry = _ref2[1];
150
-
151
- cacheEntry.sessionIds.delete(sessionId);
152
-
153
- if (cacheEntry.sessionIds.size === 0) {
154
- deleteCount += 1;
155
- delete adapterCache[cacheKey];
156
- }
157
- });
158
- } else {
159
- // otherwise call freeResources on all the cached data adapters
160
- Object.values(adapterCache).forEach(function (cacheEntry) {
161
- if (!cacheEntry.dataAdapter.freeResources) {
162
- console.warn(cacheEntry.dataAdapter, 'does not implement freeResources');
163
- } else {
164
- var regions = specification.regions || (specification.region ? [specification.region] : []);
165
- regions.forEach(function (region) {
166
- if (region.refName !== undefined) {
167
- cacheEntry.dataAdapter.freeResources(region);
168
- }
61
+ let deleteCount = 0;
62
+ const specKeys = Object.keys(specification);
63
+ // if we don't specify a range, delete any adapters that are
64
+ // only associated with that session
65
+ if (specKeys.length === 1 && specKeys[0] === 'sessionId') {
66
+ const { sessionId } = specification;
67
+ Object.entries(adapterCache).forEach(([cacheKey, cacheEntry]) => {
68
+ cacheEntry.sessionIds.delete(sessionId);
69
+ if (cacheEntry.sessionIds.size === 0) {
70
+ deleteCount += 1;
71
+ delete adapterCache[cacheKey];
72
+ }
73
+ });
74
+ }
75
+ else {
76
+ // otherwise call freeResources on all the cached data adapters
77
+ Object.values(adapterCache).forEach(cacheEntry => {
78
+ if (!cacheEntry.dataAdapter.freeResources) {
79
+ console.warn(cacheEntry.dataAdapter, 'does not implement freeResources');
80
+ }
81
+ else {
82
+ const regions = specification.regions ||
83
+ (specification.region ? [specification.region] : []);
84
+ regions.forEach((region) => {
85
+ if (region.refName !== undefined) {
86
+ cacheEntry.dataAdapter.freeResources(region);
87
+ }
88
+ });
89
+ }
169
90
  });
170
- }
171
- });
172
- }
173
-
174
- return deleteCount;
91
+ }
92
+ return deleteCount;
175
93
  }
176
-
94
+ exports.freeAdapterResources = freeAdapterResources;
177
95
  function clearAdapterCache() {
178
- adapterCache = {};
179
- }
96
+ adapterCache = {};
97
+ }
98
+ exports.clearAdapterCache = clearAdapterCache;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/core",
3
- "version": "1.7.11",
3
+ "version": "2.1.0",
4
4
  "description": "JBrowse 2 core libraries used by plugins",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -25,12 +25,11 @@
25
25
  "clean": "rimraf dist tsconfig.build.tsbuildinfo",
26
26
  "prebuild": "yarn clean",
27
27
  "prepack": "yarn build",
28
- "build": "babel . --root-mode upward --out-dir dist --extensions '.ts,.js,.tsx,.jsx' && cp package.json README.md ../../LICENSE dist/",
29
- "postbuild": "tsc -b tsconfig.build.json"
28
+ "build": "tsc -b tsconfig.build.json && cp package.json README.md ../../LICENSE dist/"
30
29
  },
31
30
  "dependencies": {
32
31
  "@babel/runtime": "^7.17.9",
33
- "@material-ui/icons": "^4.0.1",
32
+ "@mui/icons-material": "^5.0.1",
34
33
  "abortable-promise-cache": "^1.5.0",
35
34
  "canvas-sequencer": "^3.1.0",
36
35
  "canvas2svg": "^1.0.16",
@@ -43,37 +42,36 @@
43
42
  "dompurify": "^2.3.4",
44
43
  "escape-html": "^1.0.3",
45
44
  "fast-deep-equal": "^3.1.3",
46
- "generic-filehandle": "^2.2.2",
45
+ "generic-filehandle": "^3.0.0",
47
46
  "http-range-fetcher": "^1.4.0",
48
47
  "is-object": "^1.0.1",
49
48
  "jexl": "^2.3.0",
50
49
  "json-stable-stringify": "^1.0.1",
51
50
  "librpc-web-mod": "^1.1.5",
52
51
  "load-script2": "^2.0.5",
53
- "material-ui-popup-state": "^1.9.3",
54
- "object.fromentries": "^2.0.0",
52
+ "material-ui-popup-state": "^3.0.0",
55
53
  "rbush": "^3.0.1",
56
54
  "react-error-boundary": "^3.0.0",
57
- "react-intersection-observer": "^8.32.5",
55
+ "react-intersection-observer": "^9.3.0",
58
56
  "react-use-measure": "^2.1.1",
59
57
  "shortid": "^2.2.13",
60
58
  "svg-path-generator": "^1.1.0"
61
59
  },
62
60
  "peerDependencies": {
63
- "@material-ui/core": "^4.12.2",
64
- "@material-ui/lab": "^4.0.0-alpha.45",
65
- "@mui/x-data-grid": "^4.0.0",
66
- "mobx": "^5.0.0",
67
- "mobx-react": "^6.0.0",
68
- "mobx-state-tree": "^3.14.1",
61
+ "@mui/material": "^5.0.0",
62
+ "@mui/x-data-grid": "^5.0.0",
63
+ "mobx": "^6.0.0",
64
+ "mobx-react": "^7.0.0",
65
+ "mobx-state-tree": "^5.0.0",
69
66
  "prop-types": "^15.0.0",
70
- "react": "^17.0.0",
71
- "react-dom": "^17.0.0",
72
- "rxjs": "^6.0.0"
67
+ "react": ">=16.8.0",
68
+ "react-dom": ">=16.8.0",
69
+ "rxjs": "^6.0.0",
70
+ "tss-react": "^3.0.0"
73
71
  },
74
72
  "publishConfig": {
75
73
  "access": "public",
76
74
  "directory": "dist"
77
75
  },
78
- "gitHead": "5c21beb48a21f08b0091d293f09ac99174c48f77"
76
+ "gitHead": "0db0462fa1f9f15ab4869da085bcab032b9483c3"
79
77
  }
@@ -1,81 +1,26 @@
1
1
  "use strict";
2
-
3
- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
4
-
5
- Object.defineProperty(exports, "__esModule", {
6
- value: true
7
- });
8
- exports.default = void 0;
9
-
10
- var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
11
-
12
- var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
13
-
14
- var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
15
-
16
- var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
17
-
18
- var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
19
-
20
- var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
21
-
22
- var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
23
-
24
- var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
25
-
26
- var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
27
-
28
- var _PluggableElementBase2 = _interopRequireDefault(require("./PluggableElementBase"));
29
-
30
- function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
31
-
32
- function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
33
-
34
- var AdapterType = /*#__PURE__*/function (_PluggableElementBase) {
35
- (0, _inherits2.default)(AdapterType, _PluggableElementBase);
36
-
37
- var _super = _createSuper(AdapterType);
38
-
39
- function AdapterType(stuff) {
40
- var _this;
41
-
42
- (0, _classCallCheck2.default)(this, AdapterType);
43
- _this = _super.call(this, stuff);
44
- (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "AdapterClass", void 0);
45
- (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "getAdapterClass", void 0);
46
- (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "configSchema", void 0);
47
- (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "adapterCapabilities", void 0);
48
- (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "adapterMetadata", void 0);
49
-
50
- if ('AdapterClass' in stuff) {
51
- _this.AdapterClass = stuff.AdapterClass;
52
- _this.getAdapterClass = /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
53
- return _regenerator.default.wrap(function _callee$(_context) {
54
- while (1) {
55
- switch (_context.prev = _context.next) {
56
- case 0:
57
- return _context.abrupt("return", stuff.AdapterClass);
58
-
59
- case 1:
60
- case "end":
61
- return _context.stop();
62
- }
63
- }
64
- }, _callee);
65
- }));
66
- } else if ('getAdapterClass' in stuff) {
67
- _this.getAdapterClass = stuff.getAdapterClass;
68
- } else {
69
- throw new Error("no AdapterClass or getAdapterClass is defined for adapter type ".concat(_this.name));
2
+ var __importDefault = (this && this.__importDefault) || function (mod) {
3
+ return (mod && mod.__esModule) ? mod : { "default": mod };
4
+ };
5
+ Object.defineProperty(exports, "__esModule", { value: true });
6
+ /* eslint curly:error */
7
+ const PluggableElementBase_1 = __importDefault(require("./PluggableElementBase"));
8
+ class AdapterType extends PluggableElementBase_1.default {
9
+ constructor(stuff) {
10
+ super(stuff);
11
+ if ('AdapterClass' in stuff) {
12
+ this.AdapterClass = stuff.AdapterClass;
13
+ this.getAdapterClass = async () => stuff.AdapterClass;
14
+ }
15
+ else if ('getAdapterClass' in stuff) {
16
+ this.getAdapterClass = stuff.getAdapterClass;
17
+ }
18
+ else {
19
+ throw new Error(`no AdapterClass or getAdapterClass is defined for adapter type ${this.name}`);
20
+ }
21
+ this.configSchema = stuff.configSchema;
22
+ this.adapterCapabilities = stuff.adapterCapabilities || [];
23
+ this.adapterMetadata = stuff.adapterMetadata;
70
24
  }
71
-
72
- _this.configSchema = stuff.configSchema;
73
- _this.adapterCapabilities = stuff.adapterCapabilities || [];
74
- _this.adapterMetadata = stuff.adapterMetadata;
75
- return _this;
76
- }
77
-
78
- return (0, _createClass2.default)(AdapterType);
79
- }(_PluggableElementBase2.default);
80
-
81
- exports.default = AdapterType;
25
+ }
26
+ exports.default = AdapterType;
@@ -0,0 +1,17 @@
1
+ import React from 'react';
2
+ import { IAnyModelType } from 'mobx-state-tree';
3
+ import PluggableElementBase from './PluggableElementBase';
4
+ declare type BasicComponent = React.ComponentType<{
5
+ model: any;
6
+ }>;
7
+ declare type AddTrackWorkflowComponent = React.LazyExoticComponent<BasicComponent> | BasicComponent;
8
+ export default class AddTrackWorkflow extends PluggableElementBase {
9
+ ReactComponent: AddTrackWorkflowComponent;
10
+ stateModel: IAnyModelType;
11
+ constructor(stuff: {
12
+ name: string;
13
+ ReactComponent: AddTrackWorkflowComponent;
14
+ stateModel: IAnyModelType;
15
+ });
16
+ }
17
+ export {};
@@ -0,0 +1,20 @@
1
+ "use strict";
2
+ var __importDefault = (this && this.__importDefault) || function (mod) {
3
+ return (mod && mod.__esModule) ? mod : { "default": mod };
4
+ };
5
+ Object.defineProperty(exports, "__esModule", { value: true });
6
+ const PluggableElementBase_1 = __importDefault(require("./PluggableElementBase"));
7
+ class AddTrackWorkflow extends PluggableElementBase_1.default {
8
+ constructor(stuff) {
9
+ super(stuff);
10
+ this.ReactComponent = stuff.ReactComponent;
11
+ this.stateModel = stuff.stateModel;
12
+ if (!this.ReactComponent) {
13
+ throw new Error(`no ReactComponent defined for view ${this.name}`);
14
+ }
15
+ if (!this.stateModel) {
16
+ throw new Error(`no stateModel defined for view ${this.name}`);
17
+ }
18
+ }
19
+ }
20
+ exports.default = AddTrackWorkflow;