@jbrowse/core 1.5.1 → 1.5.5

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 (111) hide show
  1. package/BaseFeatureWidget/BaseFeatureDetail.d.ts +4 -2
  2. package/BaseFeatureWidget/BaseFeatureDetail.js +43 -16
  3. package/BaseFeatureWidget/SequenceFeatureDetails.js +5 -4
  4. package/BaseFeatureWidget/index.js +1 -1
  5. package/BaseFeatureWidget/util.js +5 -5
  6. package/PluginLoader.d.ts +25 -2
  7. package/PluginLoader.js +334 -47
  8. package/PluginManager.d.ts +6 -5
  9. package/PluginManager.js +1 -5
  10. package/ReExports/list.js +1 -1
  11. package/ReExports/material-ui-colors.js +38 -38
  12. package/ReExports/modules.d.ts +2 -0
  13. package/ReExports/modules.js +3 -0
  14. package/TextSearch/BaseResults.js +1 -1
  15. package/TextSearch/TextSearchManager.d.ts +1 -1
  16. package/TextSearch/TextSearchManager.js +0 -2
  17. package/assemblyManager/assembly.js +5 -3
  18. package/assemblyManager/index.js +4 -4
  19. package/configuration/configurationSchema.js +6 -4
  20. package/configuration/configurationSlot.js +3 -1
  21. package/configuration/index.js +4 -4
  22. package/configuration/util.js +2 -2
  23. package/data_adapters/BaseAdapter.d.ts +5 -5
  24. package/data_adapters/BaseAdapter.js +9 -18
  25. package/data_adapters/CytobandAdapter.js +4 -2
  26. package/data_adapters/dataAdapterCache.js +2 -2
  27. package/package.json +9 -8
  28. package/pluggableElementTypes/AdapterType.js +3 -1
  29. package/pluggableElementTypes/ConnectionType.js +3 -1
  30. package/pluggableElementTypes/DisplayType.js +3 -1
  31. package/pluggableElementTypes/InternetAccountType.js +3 -1
  32. package/pluggableElementTypes/PluggableElementBase.js +4 -3
  33. package/pluggableElementTypes/RpcMethodType.js +2 -4
  34. package/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  35. package/pluggableElementTypes/WidgetType.js +3 -1
  36. package/pluggableElementTypes/index.d.ts +2 -1
  37. package/pluggableElementTypes/index.js +37 -14
  38. package/pluggableElementTypes/models/BaseDisplayModel.js +2 -2
  39. package/pluggableElementTypes/models/BaseTrackModel.js +4 -3
  40. package/pluggableElementTypes/models/BaseViewModel.js +6 -2
  41. package/pluggableElementTypes/models/InternetAccountModel.d.ts +2 -2
  42. package/pluggableElementTypes/models/baseTrackConfig.js +2 -2
  43. package/pluggableElementTypes/models/index.js +14 -14
  44. package/pluggableElementTypes/renderers/BoxRendererType.js +3 -3
  45. package/pluggableElementTypes/renderers/CircularChordRendererType.js +3 -1
  46. package/pluggableElementTypes/renderers/ComparativeServerSideRendererType.js +2 -2
  47. package/pluggableElementTypes/renderers/FeatureRendererType.d.ts +1 -1
  48. package/pluggableElementTypes/renderers/FeatureRendererType.js +4 -4
  49. package/pluggableElementTypes/renderers/RendererType.js +3 -1
  50. package/pluggableElementTypes/renderers/ServerSideRendererType.js +2 -2
  51. package/pluggableElementTypes/renderers/index.d.ts +2 -1
  52. package/rpc/BaseRpcDriver.d.ts +1 -1
  53. package/rpc/BaseRpcDriver.js +3 -5
  54. package/rpc/BaseRpcDriver.test.js +1 -1
  55. package/rpc/RpcManager.d.ts +3 -3
  56. package/rpc/RpcManager.js +44 -22
  57. package/rpc/WebWorkerRpcDriver.d.ts +2 -2
  58. package/rpc/WebWorkerRpcDriver.js +5 -7
  59. package/rpc/coreRpcMethods.js +3 -3
  60. package/rpc/remoteAbortSignals.js +2 -2
  61. package/ui/App.js +2 -0
  62. package/ui/DrawerWidget.js +1 -0
  63. package/ui/EditableTypography.js +2 -2
  64. package/ui/FileSelector/FileSelector.js +2 -2
  65. package/ui/Icons.js +4 -4
  66. package/ui/Logo.js +1 -1
  67. package/ui/Menu.js +2 -2
  68. package/ui/NewSessionCards.js +2 -2
  69. package/ui/PrerenderedCanvas.d.ts +1 -0
  70. package/ui/PrerenderedCanvas.js +6 -3
  71. package/ui/SanitizedHTML.js +1 -1
  72. package/ui/SnackbarModel.d.ts +16 -0
  73. package/ui/SnackbarModel.js +56 -0
  74. package/ui/ViewContainer.js +4 -3
  75. package/ui/index.js +24 -24
  76. package/ui/theme.js +7 -5
  77. package/util/Base1DViewModel.js +2 -2
  78. package/util/aborting.js +7 -4
  79. package/util/blockTypes.js +8 -11
  80. package/util/calculateDynamicBlocks.test.js +2 -2
  81. package/util/color/cssColorsLevel4.js +1 -1
  82. package/util/color/index.js +5 -5
  83. package/util/compositeMap.js +3 -11
  84. package/util/index.d.ts +2 -1
  85. package/util/index.js +63 -36
  86. package/util/index.test.js +2 -2
  87. package/util/io/RemoteFileWithRangeCache.js +3 -3
  88. package/util/io/index.js +1 -1
  89. package/util/jexl.js +4 -1
  90. package/util/layouts/BaseLayout.d.ts +3 -0
  91. package/util/layouts/GranularRectLayout.d.ts +19 -10
  92. package/util/layouts/GranularRectLayout.js +459 -100
  93. package/util/layouts/GranularRectLayout.test.js +57 -10
  94. package/util/layouts/MultiLayout.d.ts +1 -1
  95. package/util/layouts/MultiLayout.js +0 -2
  96. package/util/layouts/PrecomputedLayout.js +2 -1
  97. package/util/layouts/PrecomputedMultiLayout.js +5 -3
  98. package/util/layouts/SceneGraph.d.ts +3 -3
  99. package/util/layouts/SceneGraph.js +0 -14
  100. package/util/layouts/index.d.ts +7 -0
  101. package/util/layouts/index.js +68 -0
  102. package/util/mst-reflection.d.ts +3 -3
  103. package/util/mst-reflection.js +3 -3
  104. package/util/offscreenCanvasPonyfill.js +1 -1
  105. package/util/range.js +1 -1
  106. package/util/simpleFeature.js +3 -3
  107. package/util/stats.js +4 -4
  108. package/util/tracks.js +10 -10
  109. package/util/types/index.d.ts +9 -1
  110. package/util/types/index.js +14 -19
  111. package/util/types/mst.js +3 -3
@@ -5,118 +5,118 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
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  Object.defineProperty(exports, "__esModule", {
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  value: true
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  });
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- Object.defineProperty(exports, "red", {
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+ Object.defineProperty(exports, "amber", {
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  enumerable: true,
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  get: function get() {
11
- return _red.default;
11
+ return _amber.default;
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  }
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  });
14
- Object.defineProperty(exports, "pink", {
14
+ Object.defineProperty(exports, "blue", {
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  enumerable: true,
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  get: function get() {
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- return _pink.default;
17
+ return _blue.default;
18
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  }
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  });
20
- Object.defineProperty(exports, "purple", {
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+ Object.defineProperty(exports, "blueGrey", {
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  enumerable: true,
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  get: function get() {
23
- return _purple.default;
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+ return _blueGrey.default;
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  }
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  });
26
- Object.defineProperty(exports, "deepPurple", {
26
+ Object.defineProperty(exports, "brown", {
27
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  enumerable: true,
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  get: function get() {
29
- return _deepPurple.default;
29
+ return _brown.default;
30
30
  }
31
31
  });
32
- Object.defineProperty(exports, "indigo", {
32
+ Object.defineProperty(exports, "cyan", {
33
33
  enumerable: true,
34
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  get: function get() {
35
- return _indigo.default;
35
+ return _cyan.default;
36
36
  }
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  });
38
- Object.defineProperty(exports, "blue", {
38
+ Object.defineProperty(exports, "deepOrange", {
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  enumerable: true,
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  get: function get() {
41
- return _blue.default;
41
+ return _deepOrange.default;
42
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  }
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  });
44
- Object.defineProperty(exports, "lightBlue", {
44
+ Object.defineProperty(exports, "deepPurple", {
45
45
  enumerable: true,
46
46
  get: function get() {
47
- return _lightBlue.default;
47
+ return _deepPurple.default;
48
48
  }
49
49
  });
50
- Object.defineProperty(exports, "cyan", {
50
+ Object.defineProperty(exports, "green", {
51
51
  enumerable: true,
52
52
  get: function get() {
53
- return _cyan.default;
53
+ return _green.default;
54
54
  }
55
55
  });
56
- Object.defineProperty(exports, "teal", {
56
+ Object.defineProperty(exports, "grey", {
57
57
  enumerable: true,
58
58
  get: function get() {
59
- return _teal.default;
59
+ return _grey.default;
60
60
  }
61
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  });
62
- Object.defineProperty(exports, "green", {
62
+ Object.defineProperty(exports, "indigo", {
63
63
  enumerable: true,
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64
  get: function get() {
65
- return _green.default;
65
+ return _indigo.default;
66
66
  }
67
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  });
68
- Object.defineProperty(exports, "lightGreen", {
68
+ Object.defineProperty(exports, "lightBlue", {
69
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  enumerable: true,
70
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  get: function get() {
71
- return _lightGreen.default;
71
+ return _lightBlue.default;
72
72
  }
73
73
  });
74
- Object.defineProperty(exports, "lime", {
74
+ Object.defineProperty(exports, "lightGreen", {
75
75
  enumerable: true,
76
76
  get: function get() {
77
- return _lime.default;
77
+ return _lightGreen.default;
78
78
  }
79
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  });
80
- Object.defineProperty(exports, "yellow", {
80
+ Object.defineProperty(exports, "lime", {
81
81
  enumerable: true,
82
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  get: function get() {
83
- return _yellow.default;
83
+ return _lime.default;
84
84
  }
85
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  });
86
- Object.defineProperty(exports, "amber", {
86
+ Object.defineProperty(exports, "orange", {
87
87
  enumerable: true,
88
88
  get: function get() {
89
- return _amber.default;
89
+ return _orange.default;
90
90
  }
91
91
  });
92
- Object.defineProperty(exports, "orange", {
92
+ Object.defineProperty(exports, "pink", {
93
93
  enumerable: true,
94
94
  get: function get() {
95
- return _orange.default;
95
+ return _pink.default;
96
96
  }
97
97
  });
98
- Object.defineProperty(exports, "deepOrange", {
98
+ Object.defineProperty(exports, "purple", {
99
99
  enumerable: true,
100
100
  get: function get() {
101
- return _deepOrange.default;
101
+ return _purple.default;
102
102
  }
103
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  });
104
- Object.defineProperty(exports, "brown", {
104
+ Object.defineProperty(exports, "red", {
105
105
  enumerable: true,
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  get: function get() {
107
- return _brown.default;
107
+ return _red.default;
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  }
109
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  });
110
- Object.defineProperty(exports, "grey", {
110
+ Object.defineProperty(exports, "teal", {
111
111
  enumerable: true,
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112
  get: function get() {
113
- return _grey.default;
113
+ return _teal.default;
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  }
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  });
116
- Object.defineProperty(exports, "blueGrey", {
116
+ Object.defineProperty(exports, "yellow", {
117
117
  enumerable: true,
118
118
  get: function get() {
119
- return _blueGrey.default;
119
+ return _yellow.default;
120
120
  }
121
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  });
122
122
 
@@ -22,6 +22,7 @@ import Plugin from '../Plugin';
22
22
  import * as coreUi from '../ui';
23
23
  import * as coreUtil from '../util';
24
24
  import * as coreColor from '../util/color';
25
+ import * as coreLayouts from '../util/layouts';
25
26
  import * as trackUtils from '../util/tracks';
26
27
  import * as coreIo from '../util/io';
27
28
  import * as coreMstReflection from '../util/mst-reflection';
@@ -129,6 +130,7 @@ declare const libs: {
129
130
  '@jbrowse/core/ui': typeof coreUi;
130
131
  '@jbrowse/core/util': typeof coreUtil;
131
132
  '@jbrowse/core/util/color': typeof coreColor;
133
+ '@jbrowse/core/util/layouts': typeof coreLayouts;
132
134
  '@jbrowse/core/util/tracks': typeof trackUtils;
133
135
  '@jbrowse/core/util/Base1DViewModel': mst.IModelType<{
134
136
  displayedRegions: mst.IArrayType<mst.IModelType<{
@@ -135,6 +135,8 @@ var coreUtil = _interopRequireWildcard(require("../util"));
135
135
 
136
136
  var coreColor = _interopRequireWildcard(require("../util/color"));
137
137
 
138
+ var coreLayouts = _interopRequireWildcard(require("../util/layouts"));
139
+
138
140
  var trackUtils = _interopRequireWildcard(require("../util/tracks"));
139
141
 
140
142
  var coreIo = _interopRequireWildcard(require("../util/io"));
@@ -225,6 +227,7 @@ var libs = {
225
227
  '@jbrowse/core/ui': coreUi,
226
228
  '@jbrowse/core/util': coreUtil,
227
229
  '@jbrowse/core/util/color': coreColor,
230
+ '@jbrowse/core/util/layouts': coreLayouts,
228
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  '@jbrowse/core/util/tracks': trackUtils,
229
232
  '@jbrowse/core/util/Base1DViewModel': _Base1DViewModel.default,
230
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  '@jbrowse/core/util/io': coreIo,
@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
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  Object.defineProperty(exports, "__esModule", {
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  value: true
7
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  });
8
- exports.RefSequenceResult = exports.default = void 0;
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+ exports.default = exports.RefSequenceResult = void 0;
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10
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  var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
11
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@@ -16,8 +16,8 @@ export interface SearchScope {
16
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  tracks?: Array<string>;
17
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  }
18
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  export default class TextSearchManager {
19
- adapterCache: QuickLRU;
20
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  pluginManager: PluginManager;
20
+ adapterCache: QuickLRU;
21
21
  constructor(pluginManager: PluginManager);
22
22
  /**
23
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  * Instantiate/initialize list of relevant adapters
@@ -28,8 +28,6 @@ var TextSearchManager = /*#__PURE__*/function () {
28
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  function TextSearchManager(pluginManager) {
29
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  (0, _classCallCheck2.default)(this, TextSearchManager);
30
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  (0, _defineProperty2.default)(this, "adapterCache", void 0);
31
- (0, _defineProperty2.default)(this, "pluginManager", void 0);
32
- this.pluginManager = pluginManager;
33
31
  this.adapterCache = new _QuickLRU.default({
34
32
  maxSize: 15
35
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  });
@@ -33,9 +33,9 @@ var _QuickLRU = _interopRequireDefault(require("../util/QuickLRU"));
33
33
 
34
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  var _excluded = ["signal", "statusCallback"];
35
35
 
36
- function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); if (enumerableOnly) { symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; }); } keys.push.apply(keys, symbols); } return keys; }
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+ function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
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- function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = arguments[i] != null ? arguments[i] : {}; if (i % 2) { ownKeys(Object(source), true).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }); } else if (Object.getOwnPropertyDescriptors) { Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)); } else { ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } } return target; }
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+ function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
39
39
 
40
40
  // Based on the UCSC Genome Browser chromosome color palette:
41
41
  // https://github.com/ucscGenomeBrowser/kent/blob/a50ed53aff81d6fb3e34e6913ce18578292bc24e/src/hg/inc/chromColors.h
@@ -300,7 +300,9 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
300
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  adapterConf: adapterConf,
301
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  self: self,
302
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  options: rest
303
- }, signal, statusCallback);
303
+ }, // signal intentionally not passed here, fixes issues like #2221.
304
+ // alternative fix #2540 was proposed but non-working currently
305
+ undefined, statusCallback);
304
306
  },
305
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306
308
  /**
@@ -5,16 +5,16 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
5
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  Object.defineProperty(exports, "__esModule", {
6
6
  value: true
7
7
  });
8
- Object.defineProperty(exports, "default", {
8
+ Object.defineProperty(exports, "assemblyConfigSchemaFactory", {
9
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  enumerable: true,
10
10
  get: function get() {
11
- return _assemblyManager.default;
11
+ return _assemblyConfigSchema.default;
12
12
  }
13
13
  });
14
- Object.defineProperty(exports, "assemblyConfigSchemaFactory", {
14
+ Object.defineProperty(exports, "default", {
15
15
  enumerable: true,
16
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  get: function get() {
17
- return _assemblyConfigSchema.default;
17
+ return _assemblyManager.default;
18
18
  }
19
19
  });
20
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@@ -5,8 +5,8 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
5
5
  Object.defineProperty(exports, "__esModule", {
6
6
  value: true
7
7
  });
8
- exports.ConfigurationSchema = ConfigurationSchema;
9
8
  exports.ConfigurationReference = ConfigurationReference;
9
+ exports.ConfigurationSchema = ConfigurationSchema;
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11
11
  var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
12
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@@ -22,9 +22,9 @@ var _configurationSlot = _interopRequireDefault(require("./configurationSlot"));
22
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23
23
  var _util = require("./util");
24
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25
- function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); if (enumerableOnly) { symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; }); } keys.push.apply(keys, symbols); } return keys; }
25
+ function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
26
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27
- function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = arguments[i] != null ? arguments[i] : {}; if (i % 2) { ownKeys(Object(source), true).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }); } else if (Object.getOwnPropertyDescriptors) { Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)); } else { ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } } return target; }
27
+ function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
28
28
 
29
29
  function isEmptyObject(thing) {
30
30
  return (0, _typeof2.default)(thing) === 'object' && !Array.isArray(thing) && thing !== null && Object.keys(thing).length === 0;
@@ -141,7 +141,9 @@ function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
141
141
  });
142
142
 
143
143
  if (Object.keys(volatileConstants).length) {
144
- completeModel = completeModel.volatile(function () {
144
+ completeModel = completeModel.volatile(function
145
+ /* self */
146
+ () {
145
147
  return volatileConstants;
146
148
  });
147
149
  }
@@ -16,7 +16,9 @@ var _jexlStrings = require("../util/jexlStrings");
16
16
  var _mst = require("../util/types/mst");
17
17
 
18
18
  /* eslint-disable @typescript-eslint/no-explicit-any */
19
- function isValidColorString() {
19
+ function
20
+ /* str */
21
+ isValidColorString() {
20
22
  // TODO: check all the crazy cases for whether it's a valid HTML/CSS color string
21
23
  return true;
22
24
  }
@@ -7,16 +7,16 @@ var _exportNames = {
7
7
  ConfigurationSchema: true,
8
8
  ConfigurationReference: true
9
9
  };
10
- Object.defineProperty(exports, "ConfigurationSchema", {
10
+ Object.defineProperty(exports, "ConfigurationReference", {
11
11
  enumerable: true,
12
12
  get: function get() {
13
- return _configurationSchema.ConfigurationSchema;
13
+ return _configurationSchema.ConfigurationReference;
14
14
  }
15
15
  });
16
- Object.defineProperty(exports, "ConfigurationReference", {
16
+ Object.defineProperty(exports, "ConfigurationSchema", {
17
17
  enumerable: true,
18
18
  get: function get() {
19
- return _configurationSchema.ConfigurationReference;
19
+ return _configurationSchema.ConfigurationSchema;
20
20
  }
21
21
  });
22
22
 
@@ -5,13 +5,13 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
5
5
  Object.defineProperty(exports, "__esModule", {
6
6
  value: true
7
7
  });
8
- exports.readConfObject = readConfObject;
9
8
  exports.getConf = getConf;
10
9
  exports.getTypeNamesFromExplicitlyTypedUnion = getTypeNamesFromExplicitlyTypedUnion;
11
10
  exports.isBareConfigurationSchemaType = isBareConfigurationSchemaType;
12
- exports.isConfigurationSchemaType = isConfigurationSchemaType;
13
11
  exports.isConfigurationModel = isConfigurationModel;
12
+ exports.isConfigurationSchemaType = isConfigurationSchemaType;
14
13
  exports.isConfigurationSlotType = isConfigurationSlotType;
14
+ exports.readConfObject = readConfObject;
15
15
 
16
16
  var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
17
17
 
@@ -2,7 +2,7 @@ import { Observable } from 'rxjs';
2
2
  import { Feature } from '../util/simpleFeature';
3
3
  import { AnyConfigurationModel } from '../configuration/configurationSchema';
4
4
  import { getSubAdapterType } from './dataAdapterCache';
5
- import { Region, NoAssemblyRegion } from '../util/types';
5
+ import { AugmentedRegion as Region, NoAssemblyRegion } from '../util/types';
6
6
  import BaseResult from '../TextSearch/BaseResults';
7
7
  import PluginManager from '../PluginManager';
8
8
  export interface BaseOptions {
@@ -26,12 +26,12 @@ export interface AnyAdapter {
26
26
  }
27
27
  export declare type AnyDataAdapter = BaseAdapter | BaseFeatureDataAdapter | BaseRefNameAliasAdapter | BaseTextSearchAdapter | RegionsAdapter | SequenceAdapter;
28
28
  export declare abstract class BaseAdapter {
29
+ config: AnyConfigurationModel;
30
+ getSubAdapter?: getSubAdapterType | undefined;
31
+ pluginManager?: PluginManager | undefined;
29
32
  id: string;
30
33
  static capabilities: string[];
31
- config: AnyConfigurationModel;
32
- getSubAdapter?: getSubAdapterType;
33
- pluginManager: PluginManager | undefined;
34
- constructor(config?: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
34
+ constructor(config?: AnyConfigurationModel, getSubAdapter?: getSubAdapterType | undefined, pluginManager?: PluginManager | undefined);
35
35
  /**
36
36
  * Called to provide a hint that data tied to a certain region will not be
37
37
  * needed for the forseeable future and can be purged from caches, etc
@@ -5,12 +5,12 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
5
5
  Object.defineProperty(exports, "__esModule", {
6
6
  value: true
7
7
  });
8
- exports.isSequenceAdapter = isSequenceAdapter;
9
- exports.isRegionsAdapter = isRegionsAdapter;
8
+ exports.BaseFeatureDataAdapter = exports.BaseAdapter = void 0;
10
9
  exports.isFeatureAdapter = isFeatureAdapter;
11
10
  exports.isRefNameAliasAdapter = isRefNameAliasAdapter;
11
+ exports.isRegionsAdapter = isRegionsAdapter;
12
+ exports.isSequenceAdapter = isSequenceAdapter;
12
13
  exports.isTextSearchAdapter = isTextSearchAdapter;
13
- exports.BaseFeatureDataAdapter = exports.BaseAdapter = void 0;
14
14
 
15
15
  var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
16
16
 
@@ -18,14 +18,14 @@ var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers
18
18
 
19
19
  var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
20
20
 
21
- var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
22
-
23
21
  var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
24
22
 
25
23
  var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
26
24
 
27
25
  var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
28
26
 
27
+ var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
28
+
29
29
  var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
30
30
 
31
31
  var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
@@ -50,20 +50,12 @@ function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflec
50
50
 
51
51
  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; } }
52
52
 
53
- var BaseAdapter = function BaseAdapter() {
54
- var config = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : (0, _configurationSchema.ConfigurationSchema)('empty', {}).create();
55
- var getSubAdapter = arguments.length > 1 ? arguments[1] : undefined;
56
- var pluginManager = arguments.length > 2 ? arguments[2] : undefined;
53
+ var BaseAdapter = /*#__PURE__*/(0, _createClass2.default)(function BaseAdapter(config = (0, _configurationSchema.ConfigurationSchema)('empty', {}).create(), getSubAdapter, pluginManager) {
57
54
  (0, _classCallCheck2.default)(this, BaseAdapter);
58
55
  (0, _defineProperty2.default)(this, "id", void 0);
59
- (0, _defineProperty2.default)(this, "config", void 0);
60
- (0, _defineProperty2.default)(this, "getSubAdapter", void 0);
61
- (0, _defineProperty2.default)(this, "pluginManager", void 0);
62
- this.config = config;
63
- this.getSubAdapter = getSubAdapter;
64
- this.pluginManager = pluginManager; // note: we use switch on jest here for more simple feature IDs
65
- // in test environment
66
56
 
57
+ // note: we use switch on jest here for more simple feature IDs
58
+ // in test environment
67
59
  if (typeof jest === 'undefined') {
68
60
  var data = (0, _mobxStateTree.isStateTreeNode)(config) ? (0, _mobxStateTree.getSnapshot)(config) : config;
69
61
  this.id = "".concat((0, _idMaker.default)(data));
@@ -76,13 +68,12 @@ var BaseAdapter = function BaseAdapter() {
76
68
  * needed for the forseeable future and can be purged from caches, etc
77
69
  * @param region - Region
78
70
  */
79
- ;
71
+ );
80
72
  /**
81
73
  * Base class for feature adapters to extend. Defines some methods that
82
74
  * subclasses must implement.
83
75
  */
84
76
 
85
-
86
77
  exports.BaseAdapter = BaseAdapter;
87
78
  (0, _defineProperty2.default)(BaseAdapter, "capabilities", []);
88
79
 
@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
5
5
  Object.defineProperty(exports, "__esModule", {
6
6
  value: true
7
7
  });
8
- exports.DataAdapter = exports.configSchema = void 0;
8
+ exports.configSchema = exports.DataAdapter = void 0;
9
9
 
10
10
  var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
11
11
 
@@ -118,7 +118,9 @@ var CytobandAdapter = /*#__PURE__*/function (_BaseAdapter) {
118
118
  }()
119
119
  }, {
120
120
  key: "freeResources",
121
- value: function freeResources() {}
121
+ value: function
122
+ /* { region } */
123
+ freeResources() {}
122
124
  }]);
123
125
  return CytobandAdapter;
124
126
  }(_BaseAdapter2.BaseAdapter);
@@ -5,9 +5,9 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
5
5
  Object.defineProperty(exports, "__esModule", {
6
6
  value: true
7
7
  });
8
- exports.getAdapter = getAdapter;
9
- exports.freeAdapterResources = freeAdapterResources;
10
8
  exports.clearAdapterCache = clearAdapterCache;
9
+ exports.freeAdapterResources = freeAdapterResources;
10
+ exports.getAdapter = getAdapter;
11
11
 
12
12
  var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
13
13
 
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/core",
3
- "version": "1.5.1",
3
+ "version": "1.5.5",
4
4
  "description": "JBrowse 2 core libraries used by plugins",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -30,7 +30,7 @@
30
30
  "postpublish": "git push origin main --follow-tags"
31
31
  },
32
32
  "dependencies": {
33
- "@babel/runtime": "^7.15.3",
33
+ "@babel/runtime": "^7.16.3",
34
34
  "@material-ui/icons": "^4.0.1",
35
35
  "abortable-promise-cache": "^1.1.3",
36
36
  "base64-js": "^1.3.0",
@@ -40,26 +40,27 @@
40
40
  "copy-to-clipboard": "^3.3.1",
41
41
  "deepmerge": "^4.2.2",
42
42
  "detect-node": "^2.1.0",
43
- "dompurify": "^2.0.11",
43
+ "dompurify": "^2.3.4",
44
44
  "escape-html": "^1.0.3",
45
45
  "fast-deep-equal": "^3.1.3",
46
46
  "file-uri-to-path": "^1.0.0",
47
- "generic-filehandle": "^2.2.0",
47
+ "generic-filehandle": "^2.2.2",
48
48
  "http-range-fetcher": "^1.2.2",
49
49
  "is-object": "^1.0.1",
50
50
  "jexl": "^2.3.0",
51
51
  "json-stable-stringify": "^1.0.1",
52
- "librpc-web-mod": "^1.1.2",
52
+ "librpc-web-mod": "^1.1.4",
53
53
  "load-script2": "^2.0.5",
54
54
  "object.fromentries": "^2.0.0",
55
55
  "rbush": "^3.0.1",
56
56
  "react-error-boundary": "^3.0.0",
57
- "react-intersection-observer": "^8.31.0",
57
+ "react-intersection-observer": "^8.32.5",
58
58
  "react-measure": "^2.3.0",
59
+ "sanitize-filename": "^1.6.3",
59
60
  "shortid": "^2.2.13",
60
61
  "svg-path-generator": "^1.1.0",
61
62
  "tenacious-fetch": "^2.1.0",
62
- "util.promisify": "^1.0.0"
63
+ "util.promisify": "^1.1.1"
63
64
  },
64
65
  "peerDependencies": {
65
66
  "@material-ui/core": "^4.12.2",
@@ -77,5 +78,5 @@
77
78
  "access": "public",
78
79
  "directory": "dist"
79
80
  },
80
- "gitHead": "284e408c72a3d4d7a0d603197501a8fc8f68c4bc"
81
+ "gitHead": "214a3bed2d2722f0971c0d0eed37c8d801f086d7"
81
82
  }
@@ -11,6 +11,8 @@ var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"))
11
11
 
12
12
  var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
13
13
 
14
+ var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
15
+
14
16
  var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
15
17
 
16
18
  var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
@@ -73,7 +75,7 @@ var AdapterType = /*#__PURE__*/function (_PluggableElementBase) {
73
75
  return _this;
74
76
  }
75
77
 
76
- return AdapterType;
78
+ return (0, _createClass2.default)(AdapterType);
77
79
  }(_PluggableElementBase2.default);
78
80
 
79
81
  exports.default = AdapterType;
@@ -7,6 +7,8 @@ Object.defineProperty(exports, "__esModule", {
7
7
  });
8
8
  exports.default = void 0;
9
9
 
10
+ var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
11
+
10
12
  var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
11
13
 
12
14
  var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
@@ -59,7 +61,7 @@ var ConnectionType = /*#__PURE__*/function (_PluggableElementBase) {
59
61
  return _this;
60
62
  }
61
63
 
62
- return ConnectionType;
64
+ return (0, _createClass2.default)(ConnectionType);
63
65
  }(_PluggableElementBase2.default);
64
66
 
65
67
  exports.default = ConnectionType;
@@ -7,6 +7,8 @@ Object.defineProperty(exports, "__esModule", {
7
7
  });
8
8
  exports.default = void 0;
9
9
 
10
+ var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
11
+
10
12
  var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
11
13
 
12
14
  var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
@@ -76,7 +78,7 @@ var DisplayType = /*#__PURE__*/function (_PluggableElementBase) {
76
78
  return _this;
77
79
  }
78
80
 
79
- return DisplayType;
81
+ return (0, _createClass2.default)(DisplayType);
80
82
  }(_PluggableElementBase2.default);
81
83
 
82
84
  exports.default = DisplayType;
@@ -7,6 +7,8 @@ Object.defineProperty(exports, "__esModule", {
7
7
  });
8
8
  exports.default = void 0;
9
9
 
10
+ var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
11
+
10
12
  var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
11
13
 
12
14
  var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
@@ -58,7 +60,7 @@ var InternetAccountType = /*#__PURE__*/function (_PluggableElementBase) {
58
60
  return _this;
59
61
  }
60
62
 
61
- return InternetAccountType;
63
+ return (0, _createClass2.default)(InternetAccountType);
62
64
  }(_PluggableElementBase2.default);
63
65
 
64
66
  exports.default = InternetAccountType;
@@ -7,14 +7,15 @@ Object.defineProperty(exports, "__esModule", {
7
7
  });
8
8
  exports.default = void 0;
9
9
 
10
+ var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
11
+
10
12
  var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
11
13
 
12
14
  var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
13
15
 
14
- var PluggableElementBase = function PluggableElementBase(args) {
16
+ var PluggableElementBase = /*#__PURE__*/(0, _createClass2.default)(function PluggableElementBase(args) {
15
17
  (0, _classCallCheck2.default)(this, PluggableElementBase);
16
18
  (0, _defineProperty2.default)(this, "name", '');
17
19
  this.name = args.name;
18
- };
19
-
20
+ });
20
21
  exports.default = PluggableElementBase;