@jbrowse/core 1.5.3 → 1.5.7

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Files changed (150) hide show
  1. package/BaseFeatureWidget/BaseFeatureDetail.d.ts +4 -2
  2. package/BaseFeatureWidget/BaseFeatureDetail.js +113 -100
  3. package/BaseFeatureWidget/SequenceFeatureDetails.js +59 -66
  4. package/BaseFeatureWidget/SequenceFeatureDetails.test.js +9 -9
  5. package/BaseFeatureWidget/index.js +1 -1
  6. package/BaseFeatureWidget/index.test.js +3 -3
  7. package/BaseFeatureWidget/types.js +5 -1
  8. package/BaseFeatureWidget/util.js +9 -13
  9. package/CorePlugin.js +19 -31
  10. package/Plugin.js +11 -13
  11. package/PluginLoader.js +33 -38
  12. package/PluginManager.d.ts +5 -5
  13. package/PluginManager.js +55 -60
  14. package/ReExports/index.js +4 -4
  15. package/ReExports/list.js +2 -2
  16. package/ReExports/material-ui-colors.js +20 -20
  17. package/ReExports/modules.js +47 -51
  18. package/TextSearch/BaseResults.js +24 -34
  19. package/TextSearch/BaseResults.test.js +3 -7
  20. package/TextSearch/TextSearchManager.d.ts +1 -1
  21. package/TextSearch/TextSearchManager.js +15 -18
  22. package/assemblyManager/assembly.js +34 -39
  23. package/assemblyManager/assemblyConfigSchema.js +2 -2
  24. package/assemblyManager/assemblyManager.js +16 -20
  25. package/assemblyManager/index.js +3 -3
  26. package/configuration/configurationSchema.js +17 -19
  27. package/configuration/configurationSlot.js +11 -11
  28. package/configuration/configurationSlot.test.js +5 -5
  29. package/configuration/util.js +5 -5
  30. package/data_adapters/BaseAdapter.d.ts +4 -4
  31. package/data_adapters/BaseAdapter.js +36 -47
  32. package/data_adapters/BaseAdapter.test.js +24 -30
  33. package/data_adapters/CytobandAdapter.js +16 -22
  34. package/data_adapters/dataAdapterCache.js +9 -9
  35. package/package.json +7 -7
  36. package/pluggableElementTypes/AdapterType.js +22 -29
  37. package/pluggableElementTypes/ConnectionType.js +18 -26
  38. package/pluggableElementTypes/DisplayType.js +17 -25
  39. package/pluggableElementTypes/InternetAccountType.js +14 -22
  40. package/pluggableElementTypes/PluggableElementBase.js +9 -10
  41. package/pluggableElementTypes/RpcMethodType.js +40 -56
  42. package/pluggableElementTypes/RpcMethodType.test.js +17 -23
  43. package/pluggableElementTypes/TextSearchAdapterType.js +15 -23
  44. package/pluggableElementTypes/TrackType.js +15 -25
  45. package/pluggableElementTypes/ViewType.js +15 -25
  46. package/pluggableElementTypes/WidgetType.js +17 -25
  47. package/pluggableElementTypes/index.js +11 -11
  48. package/pluggableElementTypes/models/BaseConnectionModelFactory.js +5 -5
  49. package/pluggableElementTypes/models/BaseDisplayModel.js +5 -8
  50. package/pluggableElementTypes/models/BaseTrackModel.js +8 -11
  51. package/pluggableElementTypes/models/BaseViewModel.js +3 -3
  52. package/pluggableElementTypes/models/InternetAccountModel.js +5 -5
  53. package/pluggableElementTypes/models/baseConnectionConfig.js +2 -2
  54. package/pluggableElementTypes/models/baseTrackConfig.js +4 -7
  55. package/pluggableElementTypes/models/index.js +4 -4
  56. package/pluggableElementTypes/renderers/BoxRendererType.js +39 -49
  57. package/pluggableElementTypes/renderers/CircularChordRendererType.js +12 -16
  58. package/pluggableElementTypes/renderers/ComparativeServerSideRendererType.js +27 -35
  59. package/pluggableElementTypes/renderers/FeatureRendererType.js +36 -46
  60. package/pluggableElementTypes/renderers/RendererType.js +21 -31
  61. package/pluggableElementTypes/renderers/ServerSideRenderedContent.js +8 -12
  62. package/pluggableElementTypes/renderers/ServerSideRendererType.js +31 -44
  63. package/pluggableElementTypes/renderers/index.js +8 -8
  64. package/pluggableElementTypes/renderers/util/serializableFilterChain.js +8 -10
  65. package/pluggableElementTypes/renderers/util/serializableFilterChain.test.js +2 -2
  66. package/rpc/BaseRpcDriver.d.ts +1 -1
  67. package/rpc/BaseRpcDriver.js +37 -42
  68. package/rpc/BaseRpcDriver.test.js +49 -63
  69. package/rpc/MainThreadRpcDriver.js +22 -32
  70. package/rpc/RpcManager.d.ts +2 -2
  71. package/rpc/RpcManager.js +20 -25
  72. package/rpc/WebWorkerRpcDriver.d.ts +2 -2
  73. package/rpc/WebWorkerRpcDriver.js +29 -40
  74. package/rpc/configSchema.js +2 -2
  75. package/rpc/coreRpcMethods.js +72 -82
  76. package/rpc/remoteAbortSignals.js +3 -3
  77. package/ui/AboutDialog.js +17 -21
  78. package/ui/App.js +38 -42
  79. package/ui/AssemblySelector.js +5 -5
  80. package/ui/Drawer.js +7 -7
  81. package/ui/DrawerWidget.js +33 -37
  82. package/ui/DropDownMenu.js +9 -21
  83. package/ui/EditableTypography.js +19 -30
  84. package/ui/ErrorMessage.js +5 -5
  85. package/ui/FactoryResetDialog.js +8 -8
  86. package/ui/FatalErrorDialog.js +12 -29
  87. package/ui/FatalErrorDialog.test.js +11 -11
  88. package/ui/FileSelector/FileSelector.js +32 -42
  89. package/ui/FileSelector/LocalFileChooser.js +9 -9
  90. package/ui/FileSelector/UrlChooser.js +4 -4
  91. package/ui/FileSelector/index.js +4 -4
  92. package/ui/Icons.js +9 -9
  93. package/ui/Logo.js +19 -19
  94. package/ui/Menu.js +35 -46
  95. package/ui/NewSessionCards.js +19 -29
  96. package/ui/PrerenderedCanvas.js +10 -27
  97. package/ui/ResizeHandle.js +10 -17
  98. package/ui/SanitizedHTML.js +5 -5
  99. package/ui/SanitizedHTML.test.js +4 -4
  100. package/ui/Snackbar.js +12 -16
  101. package/ui/SnackbarModel.js +1 -1
  102. package/ui/Tooltip.js +7 -11
  103. package/ui/ViewContainer.js +20 -30
  104. package/ui/index.js +13 -17
  105. package/ui/theme.js +11 -15
  106. package/util/Base1DViewModel.js +10 -14
  107. package/util/Base1DViewModel.test.js +5 -5
  108. package/util/QuickLRU.js +27 -31
  109. package/util/aborting.js +16 -24
  110. package/util/analytics.js +7 -7
  111. package/util/blockTypes.js +36 -49
  112. package/util/calculateDynamicBlocks.js +4 -4
  113. package/util/calculateDynamicBlocks.test.js +10 -14
  114. package/util/calculateStaticBlocks.js +1 -1
  115. package/util/calculateStaticBlocks.test.js +15 -15
  116. package/util/compositeMap.js +30 -41
  117. package/util/idMaker.js +4 -4
  118. package/util/index.js +35 -48
  119. package/util/index.test.js +7 -11
  120. package/util/io/RemoteFileWithRangeCache.js +29 -41
  121. package/util/io/index.js +6 -6
  122. package/util/jexl.js +8 -5
  123. package/util/jexlStrings.js +2 -2
  124. package/util/jexlStrings.test.js +2 -2
  125. package/util/layouts/BaseLayout.js +5 -1
  126. package/util/layouts/GranularRectLayout.js +28 -34
  127. package/util/layouts/GranularRectLayout.test.js +10 -10
  128. package/util/layouts/MultiLayout.d.ts +1 -1
  129. package/util/layouts/MultiLayout.js +14 -21
  130. package/util/layouts/PrecomputedLayout.js +14 -16
  131. package/util/layouts/PrecomputedMultiLayout.js +18 -22
  132. package/util/layouts/SceneGraph.d.ts +3 -3
  133. package/util/layouts/SceneGraph.js +17 -31
  134. package/util/layouts/index.js +6 -6
  135. package/util/mst-reflection.d.ts +3 -3
  136. package/util/offscreenCanvasPonyfill.js +29 -31
  137. package/util/offscreenCanvasUtils.js +6 -6
  138. package/util/range.test.js +20 -20
  139. package/util/rxjs.js +2 -2
  140. package/util/simpleFeature.js +19 -24
  141. package/util/simpleFeature.test.js +3 -3
  142. package/util/stats.js +7 -11
  143. package/util/stats.test.js +15 -15
  144. package/util/types/index.d.ts +2 -0
  145. package/util/types/index.js +29 -36
  146. package/util/types/mst.js +15 -19
  147. package/util/types/util.js +5 -1
  148. package/util/when.js +6 -6
  149. package/babel.config.d.ts +0 -15
  150. package/babel.config.js +0 -19
package/util/types/mst.js CHANGED
@@ -1,15 +1,15 @@
1
1
  "use strict";
2
2
 
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- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
3
+ var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
4
4
 
5
5
  Object.defineProperty(exports, "__esModule", {
6
6
  value: true
7
7
  });
8
8
  exports.UriLocationRaw = exports.UriLocation = exports.Region = exports.PropTypes = exports.NoAssemblyRegion = exports.LocalPathLocation = exports.FileLocation = exports.ElementId = exports.BlobLocation = void 0;
9
9
 
10
- var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
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+ var _objectSpread2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/objectSpread2.js"));
11
11
 
12
- var _objectWithoutProperties2 = _interopRequireDefault(require("@babel/runtime/helpers/objectWithoutProperties"));
12
+ var _objectWithoutProperties2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/objectWithoutProperties.js"));
13
13
 
14
14
  var _shortid = _interopRequireDefault(require("shortid"));
15
15
 
@@ -22,24 +22,20 @@ var _mobxReact = require("mobx-react");
22
22
  var _excluded = ["baseUri"],
23
23
  _excluded2 = ["locationType"];
24
24
 
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; }
26
-
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; }
28
-
29
- var ElementId = _mobxStateTree.types.optional(_mobxStateTree.types.identifier, _shortid.default.generate); // PropTypes that are useful when working with instances of these in react components
25
+ var ElementId = _mobxStateTree.types.optional(_mobxStateTree.types.identifier, _shortid["default"].generate); // PropTypes that are useful when working with instances of these in react components
30
26
 
31
27
 
32
28
  exports.ElementId = ElementId;
33
29
  var PropTypes = {
34
- Region: _propTypes.default.shape({
35
- refName: _propTypes.default.string.isRequired,
36
- start: _propTypes.default.number.isRequired,
37
- end: _propTypes.default.number.isRequired
30
+ Region: _propTypes["default"].shape({
31
+ refName: _propTypes["default"].string.isRequired,
32
+ start: _propTypes["default"].number.isRequired,
33
+ end: _propTypes["default"].number.isRequired
38
34
  }),
39
35
  ConfigSchema: _mobxReact.PropTypes.objectOrObservableObject,
40
- Feature: _propTypes.default.shape({
41
- get: _propTypes.default.func.isRequired,
42
- id: _propTypes.default.func.isRequired
36
+ Feature: _propTypes["default"].shape({
37
+ get: _propTypes["default"].func.isRequired,
38
+ id: _propTypes["default"].func.isRequired
43
39
  })
44
40
  };
45
41
  exports.PropTypes = PropTypes;
@@ -48,7 +44,7 @@ var NoAssemblyRegion = _mobxStateTree.types.model('NoAssemblyRegion', {
48
44
  refName: _mobxStateTree.types.string,
49
45
  start: _mobxStateTree.types.number,
50
46
  end: _mobxStateTree.types.number,
51
- reversed: _mobxStateTree.types.optional(_mobxStateTree.types.boolean, false)
47
+ reversed: _mobxStateTree.types.optional(_mobxStateTree.types["boolean"], false)
52
48
  }).actions(function (self) {
53
49
  return {
54
50
  setRefName: function setRefName(newRefName) {
@@ -99,7 +95,7 @@ exports.UriLocationRaw = UriLocationRaw;
99
95
  var UriLocation = _mobxStateTree.types.snapshotProcessor(UriLocationRaw, {
100
96
  postProcessor: function postProcessor(snap) {
101
97
  var baseUri = snap.baseUri,
102
- rest = (0, _objectWithoutProperties2.default)(snap, _excluded);
98
+ rest = (0, _objectWithoutProperties2["default"])(snap, _excluded);
103
99
 
104
100
  if (!baseUri) {
105
101
  return rest;
@@ -120,7 +116,7 @@ var FileLocation = _mobxStateTree.types.snapshotProcessor(_mobxStateTree.types.u
120
116
 
121
117
 
122
118
  var locationType = snapshot.locationType,
123
- rest = (0, _objectWithoutProperties2.default)(snapshot, _excluded2);
119
+ rest = (0, _objectWithoutProperties2["default"])(snapshot, _excluded2);
124
120
 
125
121
  if (!locationType) {
126
122
  // @ts-ignore
@@ -137,7 +133,7 @@ var FileLocation = _mobxStateTree.types.snapshotProcessor(_mobxStateTree.types.u
137
133
  _locationType = 'BlobLocation';
138
134
  }
139
135
 
140
- return _objectSpread(_objectSpread({}, rest), {}, {
136
+ return (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, rest), {}, {
141
137
  locationType: _locationType
142
138
  });
143
139
  }
@@ -1 +1,5 @@
1
- "use strict";
1
+ "use strict";
2
+
3
+ Object.defineProperty(exports, "__esModule", {
4
+ value: true
5
+ });
package/util/when.js CHANGED
@@ -1,6 +1,6 @@
1
1
  "use strict";
2
2
 
3
- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
3
+ var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
4
4
 
5
5
  Object.defineProperty(exports, "__esModule", {
6
6
  value: true
@@ -8,9 +8,9 @@ Object.defineProperty(exports, "__esModule", {
8
8
  exports.when = when;
9
9
  exports.whenPresent = whenPresent;
10
10
 
11
- var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
11
+ var _index = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/regenerator/index.js"));
12
12
 
13
- var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
13
+ var _asyncToGenerator2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/asyncToGenerator.js"));
14
14
 
15
15
  var _mobx = require("mobx");
16
16
 
@@ -66,7 +66,7 @@ function when(getter) {
66
66
  finishTimeout();
67
67
  resolve(true);
68
68
  }
69
- }).catch(function (err) {
69
+ })["catch"](function (err) {
70
70
  if (!finished) {
71
71
  finished = true;
72
72
  finishTimeout();
@@ -87,10 +87,10 @@ function whenPresent(_x) {
87
87
  }
88
88
 
89
89
  function _whenPresent() {
90
- _whenPresent = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(getter) {
90
+ _whenPresent = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee(getter) {
91
91
  var opts,
92
92
  _args = arguments;
93
- return _regenerator.default.wrap(function _callee$(_context) {
93
+ return _index["default"].wrap(function _callee$(_context) {
94
94
  while (1) {
95
95
  switch (_context.prev = _context.next) {
96
96
  case 0:
package/babel.config.d.ts DELETED
@@ -1,15 +0,0 @@
1
- declare function _exports(api: any): {
2
- babelrcRoots: string[];
3
- comments: boolean;
4
- presets: (string | (string | {
5
- targets: {
6
- node: number;
7
- browsers: string[];
8
- };
9
- })[])[];
10
- ignore: string[];
11
- plugins: (string | (string | {
12
- useESModules: boolean;
13
- })[])[];
14
- };
15
- export = _exports;
package/babel.config.js DELETED
@@ -1,19 +0,0 @@
1
- "use strict";
2
-
3
- module.exports = function (api) {
4
- api.cache(false);
5
- return {
6
- babelrcRoots: ['.', './packages/*', './products/*', './plugins/*'],
7
- comments: true,
8
- presets: ['@babel/preset-typescript', '@babel/preset-react', ['@babel/preset-env', {
9
- targets: {
10
- node: 8,
11
- browsers: ['> 0.5%', 'last 2 versions']
12
- }
13
- }]],
14
- ignore: ['./node_modules', './packages/*/node_modules', './products/*/node_modules', './plugins/*/node_modules'],
15
- plugins: ['@babel/plugin-syntax-dynamic-import', '@babel/plugin-proposal-class-properties', '@babel/plugin-proposal-export-default-from', ['@babel/transform-runtime', {
16
- useESModules: false
17
- }], 'inline-import-data-uri']
18
- };
19
- };