@jbrowse/core 2.0.1 → 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 (179) hide show
  1. package/BaseFeatureWidget/BaseFeatureDetail.d.ts +6 -0
  2. package/BaseFeatureWidget/BaseFeatureDetail.js +313 -592
  3. package/BaseFeatureWidget/SequenceFeatureDetails.js +213 -479
  4. package/BaseFeatureWidget/index.js +88 -126
  5. package/BaseFeatureWidget/types.js +1 -4
  6. package/BaseFeatureWidget/util.js +40 -75
  7. package/CorePlugin.js +55 -94
  8. package/Plugin.js +9 -34
  9. package/PluginLoader.js +153 -422
  10. package/PluginManager.d.ts +17 -14
  11. package/PluginManager.js +377 -666
  12. package/ReExports/Attributes.js +3 -10
  13. package/ReExports/BaseCard.js +3 -10
  14. package/ReExports/DataGrid.js +5 -12
  15. package/ReExports/FeatureDetails.js +3 -10
  16. package/ReExports/index.js +6 -12
  17. package/ReExports/list.d.ts +5 -0
  18. package/ReExports/list.js +271 -7
  19. package/ReExports/material-ui-colors.js +15 -16
  20. package/ReExports/modules.d.ts +0 -1
  21. package/ReExports/modules.js +453 -798
  22. package/TextSearch/BaseResults.js +51 -123
  23. package/TextSearch/TextSearchManager.js +66 -144
  24. package/assemblyManager/assembly.js +280 -555
  25. package/assemblyManager/assemblyConfigSchema.js +47 -64
  26. package/assemblyManager/assemblyManager.js +126 -272
  27. package/assemblyManager/index.js +9 -22
  28. package/configuration/configurationSchema.js +167 -203
  29. package/configuration/configurationSlot.js +248 -326
  30. package/configuration/index.js +19 -35
  31. package/configuration/util.js +131 -173
  32. package/data_adapters/BaseAdapter.d.ts +2 -2
  33. package/data_adapters/BaseAdapter.js +132 -521
  34. package/data_adapters/CytobandAdapter.js +40 -126
  35. package/data_adapters/dataAdapterCache.js +77 -158
  36. package/package.json +4 -5
  37. package/pluggableElementTypes/AdapterType.js +24 -79
  38. package/pluggableElementTypes/AddTrackWorkflowType.d.ts +17 -0
  39. package/pluggableElementTypes/AddTrackWorkflowType.js +20 -0
  40. package/pluggableElementTypes/ConnectionType.js +22 -65
  41. package/pluggableElementTypes/DisplayType.js +35 -82
  42. package/pluggableElementTypes/InternetAccountType.js +23 -64
  43. package/pluggableElementTypes/PluggableElementBase.js +8 -20
  44. package/pluggableElementTypes/RpcMethodType.js +85 -427
  45. package/pluggableElementTypes/TextSearchAdapterType.js +16 -55
  46. package/pluggableElementTypes/TrackType.js +26 -70
  47. package/pluggableElementTypes/ViewType.js +21 -63
  48. package/pluggableElementTypes/WidgetType.js +21 -64
  49. package/pluggableElementTypes/index.d.ts +4 -3
  50. package/pluggableElementTypes/index.js +42 -125
  51. package/pluggableElementTypes/models/BaseConnectionModelFactory.js +28 -43
  52. package/pluggableElementTypes/models/BaseDisplayModel.js +58 -95
  53. package/pluggableElementTypes/models/BaseTrackModel.js +139 -199
  54. package/pluggableElementTypes/models/BaseViewModel.js +24 -40
  55. package/pluggableElementTypes/models/InternetAccountModel.js +116 -263
  56. package/pluggableElementTypes/models/baseConnectionConfig.js +14 -25
  57. package/pluggableElementTypes/models/baseInternetAccountConfig.js +29 -38
  58. package/pluggableElementTypes/models/baseTrackConfig.js +106 -133
  59. package/pluggableElementTypes/models/index.js +21 -70
  60. package/pluggableElementTypes/renderers/BoxRendererType.js +132 -291
  61. package/pluggableElementTypes/renderers/CircularChordRendererType.js +8 -38
  62. package/pluggableElementTypes/renderers/ComparativeServerSideRendererType.js +60 -192
  63. package/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -2
  64. package/pluggableElementTypes/renderers/FeatureRendererType.js +89 -264
  65. package/pluggableElementTypes/renderers/RendererType.js +31 -105
  66. package/pluggableElementTypes/renderers/ServerSideRenderedContent.js +61 -72
  67. package/pluggableElementTypes/renderers/ServerSideRendererType.js +112 -265
  68. package/pluggableElementTypes/renderers/index.js +19 -62
  69. package/pluggableElementTypes/renderers/util/serializableFilterChain.js +27 -65
  70. package/rpc/BaseRpcDriver.js +169 -405
  71. package/rpc/MainThreadRpcDriver.js +27 -150
  72. package/rpc/RpcManager.js +58 -159
  73. package/rpc/WebWorkerRpcDriver.js +54 -171
  74. package/rpc/configSchema.js +25 -49
  75. package/rpc/coreRpcMethods.js +221 -959
  76. package/rpc/remoteAbortSignals.js +46 -70
  77. package/tsconfig.build.tsbuildinfo +1 -1
  78. package/ui/AboutDialog.js +106 -162
  79. package/ui/App.js +157 -242
  80. package/ui/AssemblySelector.js +59 -120
  81. package/ui/CascadingMenu.js +101 -196
  82. package/ui/ColorPicker.d.ts +16 -0
  83. package/ui/ColorPicker.js +97 -0
  84. package/ui/Drawer.js +28 -61
  85. package/ui/DrawerWidget.js +108 -202
  86. package/ui/DropDownMenu.js +60 -91
  87. package/ui/EditableTypography.js +87 -149
  88. package/ui/ErrorMessage.js +41 -56
  89. package/ui/FactoryResetDialog.js +24 -57
  90. package/ui/FatalErrorDialog.js +59 -91
  91. package/ui/FileSelector/FileSelector.js +123 -189
  92. package/ui/FileSelector/LocalFileChooser.js +44 -75
  93. package/ui/FileSelector/UrlChooser.js +17 -38
  94. package/ui/FileSelector/index.js +6 -12
  95. package/ui/Icons.js +45 -69
  96. package/ui/Logo.js +57 -110
  97. package/ui/Menu.js +232 -354
  98. package/ui/PrerenderedCanvas.js +63 -87
  99. package/ui/ResizeHandle.js +87 -116
  100. package/ui/ReturnToImportFormDialog.js +32 -63
  101. package/ui/SanitizedHTML.js +64 -47
  102. package/ui/Snackbar.js +74 -101
  103. package/ui/SnackbarModel.js +37 -51
  104. package/ui/Tooltip.js +49 -76
  105. package/ui/ViewContainer.js +113 -196
  106. package/ui/colors.d.ts +10 -0
  107. package/ui/colors.js +78 -0
  108. package/ui/index.js +51 -181
  109. package/ui/react-colorful.d.ts +17 -0
  110. package/ui/react-colorful.js +455 -0
  111. package/ui/theme.js +199 -247
  112. package/util/Base1DUtils.js +163 -202
  113. package/util/Base1DViewModel.js +121 -168
  114. package/util/QuickLRU.js +84 -332
  115. package/util/TimeTraveller.d.ts +19 -0
  116. package/util/TimeTraveller.js +86 -0
  117. package/util/aborting.js +49 -127
  118. package/util/analytics.js +91 -154
  119. package/util/blockTypes.js +106 -240
  120. package/util/calculateDynamicBlocks.js +98 -128
  121. package/util/calculateStaticBlocks.js +105 -125
  122. package/util/color/cssColorsLevel4.js +156 -160
  123. package/util/color/index.js +33 -55
  124. package/util/compositeMap.js +49 -333
  125. package/util/formatFastaStrings.js +9 -14
  126. package/util/idMaker.js +18 -31
  127. package/util/index.d.ts +7 -20
  128. package/util/index.js +742 -1188
  129. package/util/io/RemoteFileWithRangeCache.js +88 -257
  130. package/util/io/index.js +95 -169
  131. package/util/jexl.js +60 -115
  132. package/util/jexlStrings.js +24 -29
  133. package/util/layouts/BaseLayout.js +1 -4
  134. package/util/layouts/GranularRectLayout.js +388 -555
  135. package/util/layouts/MultiLayout.js +41 -109
  136. package/util/layouts/PrecomputedLayout.js +56 -112
  137. package/util/layouts/PrecomputedMultiLayout.js +22 -59
  138. package/util/layouts/SceneGraph.js +127 -197
  139. package/util/layouts/index.js +29 -66
  140. package/util/mst-reflection.js +55 -71
  141. package/util/offscreenCanvasPonyfill.js +66 -134
  142. package/util/offscreenCanvasUtils.d.ts +2 -7
  143. package/util/offscreenCanvasUtils.js +49 -146
  144. package/util/range.js +29 -40
  145. package/util/rxjs.js +20 -27
  146. package/util/simpleFeature.js +88 -152
  147. package/util/stats.js +91 -151
  148. package/util/tracks.js +130 -173
  149. package/util/types/index.js +110 -179
  150. package/util/types/mst.js +91 -146
  151. package/util/types/util.js +1 -4
  152. package/util/when.js +54 -101
  153. package/BaseFeatureWidget/SequenceFeatureDetails.test.js +0 -122
  154. package/BaseFeatureWidget/index.test.js +0 -69
  155. package/TextSearch/BaseResults.test.js +0 -42
  156. package/configuration/configurationSchema.test.js +0 -266
  157. package/configuration/configurationSlot.test.js +0 -69
  158. package/configuration/util.test.js +0 -39
  159. package/data_adapters/BaseAdapter.test.js +0 -200
  160. package/declare.d.js +0 -1
  161. package/pluggableElementTypes/RpcMethodType.test.js +0 -118
  162. package/pluggableElementTypes/renderers/declare.d.js +0 -1
  163. package/pluggableElementTypes/renderers/util/serializableFilterChain.test.js +0 -20
  164. package/rpc/BaseRpcDriver.test.js +0 -540
  165. package/rpc/declaration.d.js +0 -1
  166. package/ui/FatalErrorDialog.test.js +0 -82
  167. package/ui/SanitizedHTML.test.js +0 -36
  168. package/ui/theme.test.js +0 -92
  169. package/util/Base1DViewModel.test.js +0 -130
  170. package/util/calculateDynamicBlocks.test.js +0 -74
  171. package/util/calculateStaticBlocks.test.js +0 -297
  172. package/util/declare.d.js +0 -1
  173. package/util/formatFastaStrings.test.js +0 -40
  174. package/util/index.test.js +0 -213
  175. package/util/jexlStrings.test.js +0 -48
  176. package/util/layouts/GranularRectLayout.test.js +0 -99
  177. package/util/range.test.js +0 -64
  178. package/util/simpleFeature.test.js +0 -34
  179. package/util/stats.test.js +0 -172
package/ui/AboutDialog.js CHANGED
@@ -1,168 +1,112 @@
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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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- var _typeof = require("@babel/runtime/helpers/typeof");
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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.default = AboutDialog;
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-
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- var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
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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 _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
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-
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- var _react = _interopRequireWildcard(require("react"));
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-
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- var _copyToClipboard = _interopRequireDefault(require("copy-to-clipboard"));
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-
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- var _material = require("@mui/material");
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-
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- var _Close = _interopRequireDefault(require("@mui/icons-material/Close"));
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-
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- var _mui = require("tss-react/mui");
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-
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- var _configuration = require("../configuration");
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-
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- var _util = require("../util");
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-
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- var _BaseFeatureDetail = require("../BaseFeatureWidget/BaseFeatureDetail");
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-
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- function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
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-
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- function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
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-
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- var useStyles = (0, _mui.makeStyles)()(function (theme) {
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- return {
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- closeButton: {
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- position: 'absolute',
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- right: theme.spacing(1),
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- top: theme.spacing(1),
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- color: theme.palette.grey[500]
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+ var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
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+ if (k2 === undefined) k2 = k;
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+ var desc = Object.getOwnPropertyDescriptor(m, k);
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+ if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
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+ desc = { enumerable: true, get: function() { return m[k]; } };
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  }
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- };
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+ Object.defineProperty(o, k2, desc);
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+ }) : (function(o, m, k, k2) {
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+ if (k2 === undefined) k2 = k;
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+ o[k2] = m[k];
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+ }));
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+ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
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+ Object.defineProperty(o, "default", { enumerable: true, value: v });
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+ }) : function(o, v) {
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+ o["default"] = v;
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  });
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-
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- function AboutDialog(_ref) {
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- var config = _ref.config,
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- handleClose = _ref.handleClose;
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-
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- var _useStyles = useStyles(),
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- classes = _useStyles.classes;
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-
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- var _useState = (0, _react.useState)(),
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- _useState2 = (0, _slicedToArray2.default)(_useState, 2),
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- info = _useState2[0],
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- setInfo = _useState2[1];
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-
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- var _useState3 = (0, _react.useState)(),
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- _useState4 = (0, _slicedToArray2.default)(_useState3, 2),
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- error = _useState4[0],
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- setError = _useState4[1];
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-
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- var _useState5 = (0, _react.useState)(false),
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- _useState6 = (0, _slicedToArray2.default)(_useState5, 2),
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- copied = _useState6[0],
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- setCopied = _useState6[1];
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-
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- var session = (0, _util.getSession)(config);
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- var rpcManager = session.rpcManager;
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- var conf = (0, _configuration.readConfObject)(config);
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- (0, _react.useEffect)(function () {
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- var aborter = new AbortController();
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- var signal = aborter.signal;
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- var cancelled = false;
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- (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
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- var adapterConfig, result;
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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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- _context.prev = 0;
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- adapterConfig = (0, _configuration.readConfObject)(config, 'adapter');
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- _context.next = 4;
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- return rpcManager.call(config.trackId, 'CoreGetInfo', {
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- adapterConfig: adapterConfig,
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- signal: signal
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- });
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-
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- case 4:
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- result = _context.sent;
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-
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- if (!cancelled) {
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- setInfo(result);
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- }
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-
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- _context.next = 11;
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- break;
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-
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- case 8:
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- _context.prev = 8;
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- _context.t0 = _context["catch"](0);
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-
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- if (!cancelled) {
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- console.error(_context.t0);
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- setError(_context.t0);
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- }
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-
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- case 11:
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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, null, [[0, 8]]);
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- }))();
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- return function () {
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- aborter.abort();
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- cancelled = true;
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- };
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- }, [config, rpcManager]);
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- var trackName = (0, _configuration.readConfObject)(config, 'name');
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-
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- if ((0, _configuration.readConfObject)(config, 'type') === 'ReferenceSequenceTrack') {
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- var asm = session.assemblies.find(function (a) {
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- return a.sequence === config.configuration;
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- });
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- trackName = asm ? "Reference Sequence (".concat((0, _configuration.readConfObject)(asm, 'name'), ")") : 'Reference Sequence';
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- }
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-
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- var details = typeof info === 'string' ? {
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- header: "<pre>".concat(info.replace(/</g, '&lt;').replace(/>/g, '&gt;'), "</pre>")
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- } : info || {};
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- return /*#__PURE__*/_react.default.createElement(_material.Dialog, {
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- open: true,
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- onClose: handleClose
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- }, /*#__PURE__*/_react.default.createElement(_material.DialogTitle, null, trackName, /*#__PURE__*/_react.default.createElement(_material.IconButton, {
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- className: classes.closeButton,
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- onClick: function onClick() {
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- return handleClose();
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+ var __importStar = (this && this.__importStar) || function (mod) {
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+ if (mod && mod.__esModule) return mod;
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+ var result = {};
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+ if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
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+ __setModuleDefault(result, mod);
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+ return result;
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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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+ const react_1 = __importStar(require("react"));
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+ const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
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+ const material_1 = require("@mui/material");
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+ const Close_1 = __importDefault(require("@mui/icons-material/Close"));
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+ const mui_1 = require("tss-react/mui");
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+ const configuration_1 = require("../configuration");
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+ const util_1 = require("../util");
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+ const BaseFeatureDetail_1 = require("../BaseFeatureWidget/BaseFeatureDetail");
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+ const useStyles = (0, mui_1.makeStyles)()(theme => ({
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+ closeButton: {
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+ position: 'absolute',
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+ right: theme.spacing(1),
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+ top: theme.spacing(1),
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+ color: theme.palette.grey[500],
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  },
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- size: "large"
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- }, /*#__PURE__*/_react.default.createElement(_Close.default, null))), /*#__PURE__*/_react.default.createElement(_material.DialogContent, null, /*#__PURE__*/_react.default.createElement(_BaseFeatureDetail.BaseCard, {
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- title: "Configuration"
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- }, /*#__PURE__*/_react.default.createElement(_material.Button, {
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- variant: "contained",
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- style: {
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- float: 'right'
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+ content: {
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+ minWidth: 800,
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  },
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- onClick: function onClick() {
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- (0, _copyToClipboard.default)(JSON.stringify(conf, null, 2));
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- setCopied(true);
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- setTimeout(function () {
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- return setCopied(false);
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- }, 1000);
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+ }));
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+ function AboutDialog({ config, handleClose, }) {
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+ const { classes } = useStyles();
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+ const [info, setInfo] = (0, react_1.useState)();
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+ const [error, setError] = (0, react_1.useState)();
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+ const [copied, setCopied] = (0, react_1.useState)(false);
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+ const session = (0, util_1.getSession)(config);
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+ const { rpcManager } = session;
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+ const conf = (0, configuration_1.readConfObject)(config);
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+ (0, react_1.useEffect)(() => {
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+ const aborter = new AbortController();
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+ const { signal } = aborter;
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+ let cancelled = false;
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+ (async () => {
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+ try {
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+ const adapterConfig = (0, configuration_1.readConfObject)(config, 'adapter');
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+ const result = await rpcManager.call(config.trackId, 'CoreGetInfo', {
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+ adapterConfig,
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+ signal,
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+ });
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+ if (!cancelled) {
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+ setInfo(result);
69
+ }
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+ }
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+ catch (e) {
72
+ if (!cancelled) {
73
+ console.error(e);
74
+ setError(e);
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+ }
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+ }
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+ })();
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+ return () => {
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+ aborter.abort();
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+ cancelled = true;
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+ };
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+ }, [config, rpcManager]);
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+ let trackName = (0, configuration_1.readConfObject)(config, 'name');
84
+ if ((0, configuration_1.readConfObject)(config, 'type') === 'ReferenceSequenceTrack') {
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+ const asm = session.assemblies.find(a => a.sequence === config.configuration);
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+ trackName = asm
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+ ? `Reference Sequence (${(0, configuration_1.readConfObject)(asm, 'name')})`
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+ : 'Reference Sequence';
157
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  }
158
- }, copied ? 'Copied to clipboard!' : 'Copy config'), /*#__PURE__*/_react.default.createElement(_BaseFeatureDetail.Attributes, {
159
- attributes: conf,
160
- omit: ['displays', 'baseUri', 'refNames']
161
- })), info !== null ? /*#__PURE__*/_react.default.createElement(_BaseFeatureDetail.BaseCard, {
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- title: "File info"
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- }, error ? /*#__PURE__*/_react.default.createElement(_material.Typography, {
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- color: "error"
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- }, "".concat(error)) : info === undefined ? 'Loading file data...' : /*#__PURE__*/_react.default.createElement(_BaseFeatureDetail.Attributes, {
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- attributes: details
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- })) : null));
168
- }
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+ const details = typeof info === 'string'
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+ ? {
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+ header: `<pre>${info
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+ .replace(/</g, '&lt;')
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+ .replace(/>/g, '&gt;')}</pre>`,
95
+ }
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+ : info || {};
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+ return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: handleClose, maxWidth: "xl" },
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+ react_1.default.createElement(material_1.DialogTitle, null,
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+ trackName,
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+ react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: () => handleClose(), size: "large" },
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+ react_1.default.createElement(Close_1.default, null))),
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+ react_1.default.createElement(material_1.DialogContent, { className: classes.content },
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+ react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { title: "Configuration" },
104
+ react_1.default.createElement(material_1.Button, { variant: "contained", style: { float: 'right' }, onClick: () => {
105
+ (0, copy_to_clipboard_1.default)(JSON.stringify(conf, null, 2));
106
+ setCopied(true);
107
+ setTimeout(() => setCopied(false), 1000);
108
+ } }, copied ? 'Copied to clipboard!' : 'Copy config'),
109
+ react_1.default.createElement(BaseFeatureDetail_1.Attributes, { attributes: conf, omit: ['displays', 'baseUri', 'refNames'] })),
110
+ info !== null ? (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { title: "File info" }, error ? (react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`)) : info === undefined ? ('Loading file data...') : (react_1.default.createElement(BaseFeatureDetail_1.Attributes, { attributes: details })))) : null)));
111
+ }
112
+ exports.default = AboutDialog;