@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
package/ui/App.js CHANGED
@@ -1,293 +1,189 @@
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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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+ 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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+ 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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- exports.default = void 0;
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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 _core = require("@material-ui/core");
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-
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- var _Launch = _interopRequireDefault(require("@material-ui/icons/Launch"));
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-
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- var _mobxReact = require("mobx-react");
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-
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- var _mobxStateTree = require("mobx-state-tree");
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-
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- var _configuration = require("../configuration");
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-
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- var _DrawerWidget = _interopRequireDefault(require("./DrawerWidget"));
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-
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- var _DropDownMenu = _interopRequireDefault(require("./DropDownMenu"));
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-
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- var _EditableTypography = _interopRequireDefault(require("./EditableTypography"));
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-
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- var _Logo = require("./Logo");
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-
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- var _Snackbar = _interopRequireDefault(require("./Snackbar"));
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-
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- var _ViewContainer = _interopRequireDefault(require("./ViewContainer"));
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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 __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 material_1 = require("@mui/material");
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+ const mui_1 = require("tss-react/mui");
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+ const Launch_1 = __importDefault(require("@mui/icons-material/Launch"));
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+ const mobx_react_1 = require("mobx-react");
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+ const mobx_state_tree_1 = require("mobx-state-tree");
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  // locals
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- var useStyles = (0, _core.makeStyles)(function (theme) {
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- return {
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- '@global': {
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- html: {
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- 'font-family': 'Roboto'
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- },
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-
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- /* Based on: https://www.digitalocean.com/community/tutorials/css-scrollbars */
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-
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- /* The emerging W3C standard
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- that is currently Firefox-only */
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- '*': {
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- 'scrollbar-width': 'auto',
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- 'scrollbar-color': 'rgba(0,0,0,.5) rgba(128,128,128)'
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- },
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-
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- /* Works on Chrome/Edge/Safari */
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- '*::-webkit-scrollbar': {
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- '-webkit-appearance': 'none',
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- width: '12px'
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- },
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- '*::-webkit-scrollbar-thumb': {
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- 'background-color': 'rgba(0,0,0,.5)',
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- '-webkit-box-shadow': '0 0 1px rgba(255,255,255,.5)'
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- }
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- },
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+ const configuration_1 = require("../configuration");
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+ const DrawerWidget_1 = __importDefault(require("./DrawerWidget"));
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+ const DropDownMenu_1 = __importDefault(require("./DropDownMenu"));
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+ const EditableTypography_1 = __importDefault(require("./EditableTypography"));
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+ const Logo_1 = require("./Logo");
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+ const Snackbar_1 = __importDefault(require("./Snackbar"));
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+ const ViewContainer_1 = __importDefault(require("./ViewContainer"));
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+ const useStyles = (0, mui_1.makeStyles)()(theme => ({
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  root: {
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- display: 'grid',
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- height: '100vh',
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- width: '100%'
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+ fontFamily: 'Roboto',
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+ display: 'grid',
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+ height: '100vh',
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+ width: '100%',
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  },
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  fabLeft: {
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- zIndex: 10000,
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- position: 'fixed',
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- bottom: theme.spacing(2),
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- left: theme.spacing(2)
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+ zIndex: 10000,
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+ position: 'fixed',
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+ bottom: theme.spacing(2),
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+ left: theme.spacing(2),
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  },
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  fabRight: {
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- zIndex: 10000,
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- position: 'fixed',
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- bottom: theme.spacing(2),
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- right: theme.spacing(2)
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+ zIndex: 10000,
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+ position: 'fixed',
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+ bottom: theme.spacing(2),
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+ right: theme.spacing(2),
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  },
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  menuBarAndComponents: {
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- gridColumn: 'main',
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- display: 'grid',
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- gridTemplateRows: '[menubar] min-content [components] auto',
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- height: '100vh'
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+ gridColumn: 'main',
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+ display: 'grid',
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+ gridTemplateRows: '[menubar] min-content [components] auto',
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+ height: '100vh',
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  },
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  menuBar: {
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- gridRow: 'menubar'
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+ gridRow: 'menubar',
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  },
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  components: {
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- overflowY: 'auto',
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- gridRow: 'components'
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+ overflowY: 'auto',
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+ gridRow: 'components',
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  },
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  appBar: {
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- flexGrow: 1
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+ flexGrow: 1,
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  },
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  grow: {
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- flexGrow: 1
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+ flexGrow: 1,
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  },
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  inputBase: {
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- color: theme.palette.primary.contrastText
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+ color: theme.palette.primary.contrastText,
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  },
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  inputRoot: {
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- '&:hover': {
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- backgroundColor: theme.palette.primary.light
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- }
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+ '&:hover': {
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+ backgroundColor: theme.palette.primary.light,
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+ },
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  },
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  inputFocused: {
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- borderColor: theme.palette.secondary.main,
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- backgroundColor: theme.palette.primary.light
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+ borderColor: theme.palette.secondary.main,
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+ backgroundColor: theme.palette.primary.light,
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  },
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  selectPaper: {
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- padding: theme.spacing(4)
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- }
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- };
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- });
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- var Logo = (0, _mobxReact.observer)(function (_ref) {
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- var session = _ref.session;
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- var configuration = session.configuration;
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- var logoPath = (0, _configuration.readConfObject)(configuration, 'logoPath');
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-
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- if (!(logoPath !== null && logoPath !== void 0 && logoPath.uri)) {
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- return /*#__PURE__*/_react.default.createElement(_Logo.LogoFull, {
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- variant: "white"
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- });
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- } else {
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- return /*#__PURE__*/_react.default.createElement("img", {
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- src: logoPath.uri,
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- alt: "Custom logo"
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- });
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- }
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- });
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- var App = (0, _mobxReact.observer)(function (_ref2) {
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- var _viewTypes$, _grid;
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-
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- var session = _ref2.session,
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- _ref2$HeaderButtons = _ref2.HeaderButtons,
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- HeaderButtons = _ref2$HeaderButtons === void 0 ? /*#__PURE__*/_react.default.createElement("div", null) : _ref2$HeaderButtons;
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- var classes = useStyles();
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-
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- var _getEnv = (0, _mobxStateTree.getEnv)(session),
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- pluginManager = _getEnv.pluginManager;
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-
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- var viewTypes = pluginManager.getElementTypeRecord('view').all();
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-
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- var _useState = (0, _react.useState)((_viewTypes$ = viewTypes[0]) === null || _viewTypes$ === void 0 ? void 0 : _viewTypes$.name),
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- _useState2 = (0, _slicedToArray2.default)(_useState, 2),
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- value = _useState2[0],
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- setValue = _useState2[1];
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-
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- var visibleWidget = session.visibleWidget,
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- drawerWidth = session.drawerWidth,
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- minimized = session.minimized,
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- activeWidgets = session.activeWidgets,
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- savedSessionNames = session.savedSessionNames,
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- name = session.name,
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- menus = session.menus,
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- views = session.views,
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- drawerPosition = session.drawerPosition;
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-
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- function handleNameChange(newName) {
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- if (savedSessionNames !== null && savedSessionNames !== void 0 && savedSessionNames.includes(newName)) {
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- session.notify("Cannot rename session to \"".concat(newName, "\", a saved session with that name already exists"), 'warning');
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- } else {
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- session.renameCurrentSession(newName);
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- }
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- }
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-
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- var drawerVisible = visibleWidget && !minimized;
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- var grid;
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-
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- if (drawerPosition === 'right') {
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- grid = ["[main] 1fr", drawerVisible ? "[drawer] ".concat(drawerWidth, "px") : undefined];
179
- } else if (drawerPosition === 'left') {
180
- grid = [drawerVisible ? "[drawer] ".concat(drawerWidth, "px") : undefined, "[main] 1fr"];
181
- }
182
-
183
- return /*#__PURE__*/_react.default.createElement("div", {
184
- className: classes.root,
185
- style: {
186
- gridTemplateColumns: (_grid = grid) === null || _grid === void 0 ? void 0 : _grid.filter(function (f) {
187
- return !!f;
188
- }).join(' ')
189
- }
190
- }, drawerVisible && drawerPosition === 'left' ? /*#__PURE__*/_react.default.createElement(_DrawerWidget.default, {
191
- session: session
192
- }) : null, session.DialogComponent ? /*#__PURE__*/_react.default.createElement(_react.Suspense, {
193
- fallback: /*#__PURE__*/_react.default.createElement("div", null)
194
- }, /*#__PURE__*/_react.default.createElement(session.DialogComponent, session.DialogProps)) : null, /*#__PURE__*/_react.default.createElement("div", {
195
- className: classes.menuBarAndComponents
196
- }, /*#__PURE__*/_react.default.createElement("div", {
197
- className: classes.menuBar
198
- }, /*#__PURE__*/_react.default.createElement(_core.AppBar, {
199
- className: classes.appBar,
200
- position: "static"
201
- }, /*#__PURE__*/_react.default.createElement(_core.Toolbar, null, menus.map(function (menu) {
202
- return /*#__PURE__*/_react.default.createElement(_DropDownMenu.default, {
203
- key: menu.label,
204
- menuTitle: menu.label,
205
- menuItems: menu.menuItems,
206
- session: session
207
- });
208
- }), /*#__PURE__*/_react.default.createElement("div", {
209
- className: classes.grow
210
- }), /*#__PURE__*/_react.default.createElement(_core.Tooltip, {
211
- title: "Rename Session",
212
- arrow: true
213
- }, /*#__PURE__*/_react.default.createElement(_EditableTypography.default, {
214
- value: name,
215
- setValue: handleNameChange,
216
- variant: "body1",
217
- classes: {
218
- inputBase: classes.inputBase,
219
- inputRoot: classes.inputRoot,
220
- inputFocused: classes.inputFocused
221
- }
222
- })), HeaderButtons, /*#__PURE__*/_react.default.createElement("div", {
223
- className: classes.grow
224
- }), /*#__PURE__*/_react.default.createElement("div", {
225
- style: {
226
- width: 150,
227
- maxHeight: 48
94
+ padding: theme.spacing(4),
95
+ },
96
+ }));
97
+ const Logo = (0, mobx_react_1.observer)(({ session }) => {
98
+ const { configuration } = session;
99
+ const logoPath = (0, configuration_1.readConfObject)(configuration, 'logoPath');
100
+ if (!(logoPath === null || logoPath === void 0 ? void 0 : logoPath.uri)) {
101
+ return react_1.default.createElement(Logo_1.LogoFull, { variant: "white" });
228
102
  }
229
- }, /*#__PURE__*/_react.default.createElement(Logo, {
230
- session: session
231
- }))))), /*#__PURE__*/_react.default.createElement("div", {
232
- className: classes.components
233
- }, views.length ? views.map(function (view) {
234
- var viewType = pluginManager.getViewType(view.type);
235
-
236
- if (!viewType) {
237
- throw new Error("unknown view type ".concat(view.type));
103
+ else {
104
+ return react_1.default.createElement("img", { src: logoPath.uri, alt: "Custom logo" });
238
105
  }
239
-
240
- var ReactComponent = viewType.ReactComponent;
241
- return /*#__PURE__*/_react.default.createElement(_ViewContainer.default, {
242
- key: "view-".concat(view.id),
243
- view: view,
244
- onClose: function onClose() {
245
- return session.removeView(view);
246
- }
247
- }, /*#__PURE__*/_react.default.createElement(_react.Suspense, {
248
- fallback: /*#__PURE__*/_react.default.createElement("div", null, "Loading...")
249
- }, /*#__PURE__*/_react.default.createElement(ReactComponent, {
250
- model: view,
251
- session: session,
252
- getTrackType: pluginManager.getTrackType
253
- })));
254
- }) : /*#__PURE__*/_react.default.createElement(_core.Paper, {
255
- className: classes.selectPaper
256
- }, /*#__PURE__*/_react.default.createElement(_core.Typography, null, "Select a view to launch"), /*#__PURE__*/_react.default.createElement(_core.Select, {
257
- value: value,
258
- onChange: function onChange(event) {
259
- return setValue(event.target.value);
106
+ });
107
+ const App = (0, mobx_react_1.observer)(({ session, HeaderButtons = react_1.default.createElement("div", null), }) => {
108
+ var _a;
109
+ const { classes } = useStyles();
110
+ const { pluginManager } = (0, mobx_state_tree_1.getEnv)(session);
111
+ const viewTypes = pluginManager.getElementTypeRecord('view').all();
112
+ const [value, setValue] = (0, react_1.useState)((_a = viewTypes[0]) === null || _a === void 0 ? void 0 : _a.name);
113
+ const { visibleWidget, drawerWidth, minimized, activeWidgets, savedSessionNames, name, menus, views, drawerPosition, } = session;
114
+ function handleNameChange(newName) {
115
+ if (savedSessionNames === null || savedSessionNames === void 0 ? void 0 : savedSessionNames.includes(newName)) {
116
+ session.notify(`Cannot rename session to "${newName}", a saved session with that name already exists`, 'warning');
117
+ }
118
+ else {
119
+ session.renameCurrentSession(newName);
120
+ }
260
121
  }
261
- }, viewTypes.map(function (_ref3) {
262
- var name = _ref3.name;
263
- return /*#__PURE__*/_react.default.createElement(_core.MenuItem, {
264
- key: name,
265
- value: name
266
- }, name);
267
- })), /*#__PURE__*/_react.default.createElement(_core.Button, {
268
- onClick: function onClick() {
269
- session.addView(value, {});
270
- },
271
- variant: "contained",
272
- color: "primary"
273
- }, "Launch view")), /*#__PURE__*/_react.default.createElement("div", {
274
- style: {
275
- height: 300
122
+ const drawerVisible = visibleWidget && !minimized;
123
+ let grid;
124
+ if (drawerPosition === 'right') {
125
+ grid = [
126
+ `[main] 1fr`,
127
+ drawerVisible ? `[drawer] ${drawerWidth}px` : undefined,
128
+ ];
276
129
  }
277
- }))), activeWidgets.size > 0 && minimized ? /*#__PURE__*/_react.default.createElement(_core.Tooltip, {
278
- title: "Open drawer widget"
279
- }, /*#__PURE__*/_react.default.createElement(_core.Fab, {
280
- className: drawerPosition === 'right' ? classes.fabRight : classes.fabLeft,
281
- color: "primary",
282
- "data-testid": "drawer-maximize",
283
- onClick: function onClick() {
284
- return session.showWidgetDrawer();
130
+ else if (drawerPosition === 'left') {
131
+ grid = [
132
+ drawerVisible ? `[drawer] ${drawerWidth}px` : undefined,
133
+ `[main] 1fr`,
134
+ ];
285
135
  }
286
- }, /*#__PURE__*/_react.default.createElement(_Launch.default, null))) : null, drawerVisible && drawerPosition === 'right' ? /*#__PURE__*/_react.default.createElement(_DrawerWidget.default, {
287
- session: session
288
- }) : null, /*#__PURE__*/_react.default.createElement(_Snackbar.default, {
289
- session: session
290
- }));
136
+ return (react_1.default.createElement("div", { className: classes.root, style: {
137
+ gridTemplateColumns: grid === null || grid === void 0 ? void 0 : grid.filter(f => !!f).join(' '),
138
+ } },
139
+ drawerVisible && drawerPosition === 'left' ? (react_1.default.createElement(DrawerWidget_1.default, { session: session })) : null,
140
+ session.DialogComponent ? (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
141
+ react_1.default.createElement(session.DialogComponent, { ...session.DialogProps }))) : null,
142
+ react_1.default.createElement("div", { className: classes.menuBarAndComponents },
143
+ react_1.default.createElement("div", { className: classes.menuBar },
144
+ react_1.default.createElement(material_1.AppBar, { className: classes.appBar, position: "static" },
145
+ react_1.default.createElement(material_1.Toolbar, null,
146
+ menus.map(menu => (react_1.default.createElement(DropDownMenu_1.default, { key: menu.label, menuTitle: menu.label, menuItems: menu.menuItems, session: session }))),
147
+ react_1.default.createElement("div", { className: classes.grow }),
148
+ react_1.default.createElement(material_1.Tooltip, { title: "Rename Session", arrow: true },
149
+ react_1.default.createElement(EditableTypography_1.default, { value: name, setValue: handleNameChange, variant: "body1", classes: {
150
+ inputBase: classes.inputBase,
151
+ inputRoot: classes.inputRoot,
152
+ inputFocused: classes.inputFocused,
153
+ } })),
154
+ HeaderButtons,
155
+ react_1.default.createElement("div", { className: classes.grow }),
156
+ react_1.default.createElement("div", { style: { width: 150, maxHeight: 48 } },
157
+ react_1.default.createElement(Logo, { session: session }))))),
158
+ react_1.default.createElement("div", { className: classes.components },
159
+ views.length ? (views.map(view => {
160
+ const viewType = pluginManager.getViewType(view.type);
161
+ if (!viewType) {
162
+ throw new Error(`unknown view type ${view.type}`);
163
+ }
164
+ const { ReactComponent } = viewType;
165
+ return (react_1.default.createElement(ViewContainer_1.default, { key: `view-${view.id}`, view: view, onClose: () => {
166
+ session.removeView(view);
167
+ session.notify(`A view has been closed`, 'info', {
168
+ name: 'undo',
169
+ onClick: () => {
170
+ pluginManager.rootModel.history.undo();
171
+ },
172
+ });
173
+ } },
174
+ react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null, "Loading...") },
175
+ react_1.default.createElement(ReactComponent, { model: view, session: session, getTrackType: pluginManager.getTrackType }))));
176
+ })) : (react_1.default.createElement(material_1.Paper, { className: classes.selectPaper },
177
+ react_1.default.createElement(material_1.Typography, null, "Select a view to launch"),
178
+ react_1.default.createElement(material_1.Select, { value: value, onChange: event => setValue(event.target.value) }, viewTypes.map(({ name }) => (react_1.default.createElement(material_1.MenuItem, { key: name, value: name }, name)))),
179
+ react_1.default.createElement(material_1.Button, { onClick: () => {
180
+ session.addView(value, {});
181
+ }, variant: "contained", color: "primary" }, "Launch view"))),
182
+ react_1.default.createElement("div", { style: { height: 300 } }))),
183
+ activeWidgets.size > 0 && minimized ? (react_1.default.createElement(material_1.Tooltip, { title: "Open drawer widget" },
184
+ react_1.default.createElement(material_1.Fab, { className: drawerPosition === 'right' ? classes.fabRight : classes.fabLeft, color: "primary", "data-testid": "drawer-maximize", onClick: () => session.showWidgetDrawer() },
185
+ react_1.default.createElement(Launch_1.default, null)))) : null,
186
+ drawerVisible && drawerPosition === 'right' ? (react_1.default.createElement(DrawerWidget_1.default, { session: session })) : null,
187
+ react_1.default.createElement(Snackbar_1.default, { session: session })));
291
188
  });
292
- var _default = App;
293
- exports.default = _default;
189
+ exports.default = App;
@@ -1,5 +1,5 @@
1
1
  /// <reference types="react" />
2
- import { InputProps as IIP } from '@material-ui/core';
2
+ import { InputProps as IIP } from '@mui/material';
3
3
  import { AbstractSessionModel } from '../util';
4
4
  declare const AssemblySelector: ({ session, onChange, selected, InputProps, extra, }: {
5
5
  session: AbstractSessionModel;
@@ -1,120 +1,64 @@
1
1
  "use strict";
2
-
3
- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
4
-
5
- var _typeof = require("@babel/runtime/helpers/typeof");
6
-
7
- Object.defineProperty(exports, "__esModule", {
8
- value: true
2
+ var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
3
+ if (k2 === undefined) k2 = k;
4
+ var desc = Object.getOwnPropertyDescriptor(m, k);
5
+ if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
6
+ desc = { enumerable: true, get: function() { return m[k]; } };
7
+ }
8
+ Object.defineProperty(o, k2, desc);
9
+ }) : (function(o, m, k, k2) {
10
+ if (k2 === undefined) k2 = k;
11
+ o[k2] = m[k];
12
+ }));
13
+ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
14
+ Object.defineProperty(o, "default", { enumerable: true, value: v });
15
+ }) : function(o, v) {
16
+ o["default"] = v;
9
17
  });
10
- exports.default = void 0;
11
-
12
- var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
13
-
14
- var _react = _interopRequireWildcard(require("react"));
15
-
16
- var _mobxReact = require("mobx-react");
17
-
18
- var _configuration = require("../configuration");
19
-
20
- var _core = require("@material-ui/core");
21
-
22
- 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); }
23
-
24
- 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; }
25
-
26
- var useStyles = (0, _core.makeStyles)(function () {
27
- return {
18
+ var __importStar = (this && this.__importStar) || function (mod) {
19
+ if (mod && mod.__esModule) return mod;
20
+ var result = {};
21
+ if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
22
+ __setModuleDefault(result, mod);
23
+ return result;
24
+ };
25
+ Object.defineProperty(exports, "__esModule", { value: true });
26
+ const react_1 = __importStar(require("react"));
27
+ const mobx_react_1 = require("mobx-react");
28
+ const material_1 = require("@mui/material");
29
+ const util_1 = require("@jbrowse/core/util");
30
+ const mui_1 = require("tss-react/mui");
31
+ // locals
32
+ const configuration_1 = require("../configuration");
33
+ const useStyles = (0, mui_1.makeStyles)()(() => ({
28
34
  importFormEntry: {
29
- minWidth: 180
30
- }
31
- };
32
- }); // Hook from https://usehooks.com/useLocalStorage/
33
-
34
- function useLocalStorage(key, initialValue) {
35
- var _useState = (0, _react.useState)(function () {
36
- if (typeof window === 'undefined') {
37
- return initialValue;
38
- }
39
-
40
- try {
41
- var item = window.localStorage.getItem(key);
42
- return item ? JSON.parse(item) : initialValue;
43
- } catch (error) {
44
- console.error(error);
45
- return initialValue;
46
- }
47
- }),
48
- _useState2 = (0, _slicedToArray2.default)(_useState, 2),
49
- storedValue = _useState2[0],
50
- setStoredValue = _useState2[1];
51
-
52
- var setValue = function setValue(value) {
53
- try {
54
- var valueToStore = value instanceof Function ? value(storedValue) : value;
55
- setStoredValue(valueToStore);
56
-
57
- if (typeof window !== 'undefined') {
58
- window.localStorage.setItem(key, JSON.stringify(valueToStore));
59
- }
60
- } catch (error) {
61
- console.error(error);
62
- }
63
- };
64
-
65
- return [storedValue, setValue];
66
- }
67
-
68
- var AssemblySelector = (0, _mobxReact.observer)(function (_ref) {
69
- var session = _ref.session,
70
- onChange = _ref.onChange,
71
- selected = _ref.selected,
72
- InputProps = _ref.InputProps,
73
- _ref$extra = _ref.extra,
74
- extra = _ref$extra === void 0 ? 0 : _ref$extra;
75
- var classes = useStyles();
76
- var assemblyNames = session.assemblyNames,
77
- assemblyManager = session.assemblyManager; // constructs a localstorage key based on host/path/config to help
78
- // remember. non-config assists usage with e.g. embedded apps
79
-
80
- var config = new URLSearchParams(window.location.search).get('config');
81
-
82
- var _useLocalStorage = useLocalStorage("lastAssembly-".concat([window.location.host + window.location.pathname, config, extra].join('-')), selected),
83
- _useLocalStorage2 = (0, _slicedToArray2.default)(_useLocalStorage, 2),
84
- lastSelected = _useLocalStorage2[0],
85
- setLastSelected = _useLocalStorage2[1];
86
-
87
- var selection = assemblyNames.includes(lastSelected || '') ? lastSelected : selected;
88
- (0, _react.useEffect)(function () {
89
- if (selection && selection !== selected) {
90
- onChange(selection);
91
- }
92
- }, [selection, onChange, selected]);
93
- var error = assemblyNames.length ? '' : 'No configured assemblies';
94
- return /*#__PURE__*/_react.default.createElement(_core.TextField, {
95
- select: true,
96
- label: "Assembly",
97
- variant: "outlined",
98
- helperText: error || 'Select assembly to view',
99
- value: error ? '' : selection,
100
- inputProps: {
101
- 'data-testid': 'assembly-selector'
102
- },
103
- onChange: function onChange(event) {
104
- return setLastSelected(event.target.value);
35
+ minWidth: 180,
105
36
  },
106
- error: !!error,
107
- InputProps: InputProps,
108
- disabled: !!error,
109
- className: classes.importFormEntry
110
- }, assemblyNames.map(function (name) {
111
- var assembly = assemblyManager.get(name);
112
- var displayName = assembly ? (0, _configuration.getConf)(assembly, 'displayName') : '';
113
- return /*#__PURE__*/_react.default.createElement(_core.MenuItem, {
114
- key: name,
115
- value: name
116
- }, displayName || name);
117
- }));
37
+ }));
38
+ const AssemblySelector = (0, mobx_react_1.observer)(({ session, onChange, selected, InputProps, extra = 0, }) => {
39
+ const { classes } = useStyles();
40
+ const { assemblyNames, assemblyManager } = session;
41
+ // constructs a localstorage key based on host/path/config to help
42
+ // remember. non-config assists usage with e.g. embedded apps
43
+ const config = new URLSearchParams(window.location.search).get('config');
44
+ const [lastSelected, setLastSelected] = (0, util_1.useLocalStorage)(`lastAssembly-${[
45
+ window.location.host + window.location.pathname,
46
+ config,
47
+ extra,
48
+ ].join('-')}`, selected);
49
+ const selection = assemblyNames.includes(lastSelected || '')
50
+ ? lastSelected
51
+ : selected;
52
+ (0, react_1.useEffect)(() => {
53
+ if (selection && selection !== selected) {
54
+ onChange(selection);
55
+ }
56
+ }, [selection, onChange, selected]);
57
+ const error = assemblyNames.length ? '' : 'No configured assemblies';
58
+ return (react_1.default.createElement(material_1.TextField, { select: true, label: "Assembly", variant: "outlined", helperText: error || 'Select assembly to view', value: error ? '' : selection, inputProps: { 'data-testid': 'assembly-selector' }, onChange: event => setLastSelected(event.target.value), error: !!error, InputProps: InputProps, disabled: !!error, className: classes.importFormEntry }, assemblyNames.map(name => {
59
+ const assembly = assemblyManager.get(name);
60
+ const displayName = assembly ? (0, configuration_1.getConf)(assembly, 'displayName') : '';
61
+ return (react_1.default.createElement(material_1.MenuItem, { key: name, value: name }, displayName || name));
62
+ })));
118
63
  });
119
- var _default = AssemblySelector;
120
- exports.default = _default;
64
+ exports.default = AssemblySelector;