@jbrowse/core 1.5.5 → 1.5.6

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Files changed (139) hide show
  1. package/BaseFeatureWidget/BaseFeatureDetail.js +78 -91
  2. package/BaseFeatureWidget/SequenceFeatureDetails.js +57 -65
  3. package/BaseFeatureWidget/SequenceFeatureDetails.test.js +9 -9
  4. package/BaseFeatureWidget/index.js +1 -1
  5. package/BaseFeatureWidget/index.test.js +3 -3
  6. package/BaseFeatureWidget/types.js +5 -1
  7. package/BaseFeatureWidget/util.js +9 -13
  8. package/CorePlugin.js +19 -31
  9. package/Plugin.js +11 -13
  10. package/PluginLoader.js +33 -38
  11. package/PluginManager.js +55 -56
  12. package/ReExports/index.js +4 -4
  13. package/ReExports/list.js +2 -2
  14. package/ReExports/material-ui-colors.js +20 -20
  15. package/ReExports/modules.js +47 -51
  16. package/TextSearch/BaseResults.js +24 -34
  17. package/TextSearch/BaseResults.test.js +3 -7
  18. package/TextSearch/TextSearchManager.js +16 -17
  19. package/assemblyManager/assembly.js +34 -39
  20. package/assemblyManager/assemblyConfigSchema.js +2 -2
  21. package/assemblyManager/assemblyManager.js +16 -20
  22. package/assemblyManager/index.js +3 -3
  23. package/configuration/configurationSchema.js +17 -19
  24. package/configuration/configurationSlot.js +11 -11
  25. package/configuration/configurationSlot.test.js +5 -5
  26. package/configuration/util.js +5 -5
  27. package/data_adapters/BaseAdapter.js +38 -40
  28. package/data_adapters/BaseAdapter.test.js +24 -30
  29. package/data_adapters/CytobandAdapter.js +16 -22
  30. package/data_adapters/dataAdapterCache.js +9 -9
  31. package/package.json +3 -3
  32. package/pluggableElementTypes/AdapterType.js +22 -31
  33. package/pluggableElementTypes/ConnectionType.js +18 -28
  34. package/pluggableElementTypes/DisplayType.js +17 -27
  35. package/pluggableElementTypes/InternetAccountType.js +14 -24
  36. package/pluggableElementTypes/PluggableElementBase.js +8 -10
  37. package/pluggableElementTypes/RpcMethodType.js +41 -55
  38. package/pluggableElementTypes/RpcMethodType.test.js +17 -23
  39. package/pluggableElementTypes/TextSearchAdapterType.js +15 -25
  40. package/pluggableElementTypes/TrackType.js +15 -25
  41. package/pluggableElementTypes/ViewType.js +15 -25
  42. package/pluggableElementTypes/WidgetType.js +17 -27
  43. package/pluggableElementTypes/index.js +11 -11
  44. package/pluggableElementTypes/models/BaseConnectionModelFactory.js +5 -5
  45. package/pluggableElementTypes/models/BaseDisplayModel.js +5 -8
  46. package/pluggableElementTypes/models/BaseTrackModel.js +8 -11
  47. package/pluggableElementTypes/models/BaseViewModel.js +3 -3
  48. package/pluggableElementTypes/models/InternetAccountModel.js +5 -5
  49. package/pluggableElementTypes/models/baseConnectionConfig.js +2 -2
  50. package/pluggableElementTypes/models/baseTrackConfig.js +4 -7
  51. package/pluggableElementTypes/models/index.js +4 -4
  52. package/pluggableElementTypes/renderers/BoxRendererType.js +39 -49
  53. package/pluggableElementTypes/renderers/CircularChordRendererType.js +12 -18
  54. package/pluggableElementTypes/renderers/ComparativeServerSideRendererType.js +27 -35
  55. package/pluggableElementTypes/renderers/FeatureRendererType.js +36 -46
  56. package/pluggableElementTypes/renderers/RendererType.js +21 -31
  57. package/pluggableElementTypes/renderers/ServerSideRenderedContent.js +8 -12
  58. package/pluggableElementTypes/renderers/ServerSideRendererType.js +31 -44
  59. package/pluggableElementTypes/renderers/index.js +8 -8
  60. package/pluggableElementTypes/renderers/util/serializableFilterChain.js +8 -10
  61. package/pluggableElementTypes/renderers/util/serializableFilterChain.test.js +2 -2
  62. package/rpc/BaseRpcDriver.js +38 -41
  63. package/rpc/BaseRpcDriver.test.js +49 -63
  64. package/rpc/MainThreadRpcDriver.js +22 -32
  65. package/rpc/RpcManager.js +20 -19
  66. package/rpc/WebWorkerRpcDriver.js +29 -38
  67. package/rpc/configSchema.js +2 -2
  68. package/rpc/coreRpcMethods.js +72 -82
  69. package/rpc/remoteAbortSignals.js +3 -3
  70. package/ui/AboutDialog.js +17 -21
  71. package/ui/App.js +38 -42
  72. package/ui/AssemblySelector.js +5 -5
  73. package/ui/Drawer.js +7 -7
  74. package/ui/DrawerWidget.js +33 -37
  75. package/ui/DropDownMenu.js +9 -21
  76. package/ui/EditableTypography.js +19 -30
  77. package/ui/ErrorMessage.js +5 -5
  78. package/ui/FactoryResetDialog.js +8 -8
  79. package/ui/FatalErrorDialog.js +12 -29
  80. package/ui/FatalErrorDialog.test.js +11 -11
  81. package/ui/FileSelector/FileSelector.js +32 -42
  82. package/ui/FileSelector/LocalFileChooser.js +9 -9
  83. package/ui/FileSelector/UrlChooser.js +4 -4
  84. package/ui/FileSelector/index.js +4 -4
  85. package/ui/Icons.js +9 -9
  86. package/ui/Logo.js +19 -19
  87. package/ui/Menu.js +35 -46
  88. package/ui/NewSessionCards.js +19 -29
  89. package/ui/PrerenderedCanvas.js +10 -27
  90. package/ui/ResizeHandle.js +10 -17
  91. package/ui/SanitizedHTML.js +5 -5
  92. package/ui/SanitizedHTML.test.js +4 -4
  93. package/ui/Snackbar.js +12 -16
  94. package/ui/SnackbarModel.js +1 -1
  95. package/ui/Tooltip.js +7 -11
  96. package/ui/ViewContainer.js +20 -30
  97. package/ui/index.js +13 -17
  98. package/ui/theme.js +11 -15
  99. package/util/Base1DViewModel.js +10 -14
  100. package/util/Base1DViewModel.test.js +5 -5
  101. package/util/QuickLRU.js +27 -31
  102. package/util/aborting.js +16 -26
  103. package/util/analytics.js +7 -7
  104. package/util/blockTypes.js +39 -49
  105. package/util/calculateDynamicBlocks.js +4 -4
  106. package/util/calculateDynamicBlocks.test.js +10 -14
  107. package/util/calculateStaticBlocks.js +1 -1
  108. package/util/calculateStaticBlocks.test.js +15 -15
  109. package/util/compositeMap.js +28 -31
  110. package/util/idMaker.js +4 -4
  111. package/util/index.js +33 -44
  112. package/util/index.test.js +7 -11
  113. package/util/io/RemoteFileWithRangeCache.js +29 -41
  114. package/util/io/index.js +6 -6
  115. package/util/jexl.js +8 -5
  116. package/util/jexlStrings.js +2 -2
  117. package/util/jexlStrings.test.js +2 -2
  118. package/util/layouts/BaseLayout.js +5 -1
  119. package/util/layouts/GranularRectLayout.js +27 -33
  120. package/util/layouts/GranularRectLayout.test.js +10 -10
  121. package/util/layouts/MultiLayout.js +14 -19
  122. package/util/layouts/PrecomputedLayout.js +14 -16
  123. package/util/layouts/PrecomputedMultiLayout.js +17 -23
  124. package/util/layouts/SceneGraph.js +18 -18
  125. package/util/layouts/index.js +6 -6
  126. package/util/offscreenCanvasPonyfill.js +29 -31
  127. package/util/offscreenCanvasUtils.js +6 -6
  128. package/util/range.test.js +20 -20
  129. package/util/rxjs.js +2 -2
  130. package/util/simpleFeature.js +19 -24
  131. package/util/simpleFeature.test.js +3 -3
  132. package/util/stats.js +7 -11
  133. package/util/stats.test.js +15 -15
  134. package/util/types/index.js +32 -34
  135. package/util/types/mst.js +15 -19
  136. package/util/types/util.js +5 -1
  137. package/util/when.js +6 -6
  138. package/babel.config.d.ts +0 -15
  139. package/babel.config.js +0 -19
@@ -1,29 +1,23 @@
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- var _super = _createSuper(ServerSideRenderer);
49
+ var _super = (0, _createSuper2["default"])(ServerSideRenderer);
62
50
 
63
51
  function ServerSideRenderer() {
64
- (0, _classCallCheck2.default)(this, ServerSideRenderer);
52
+ (0, _classCallCheck2["default"])(this, ServerSideRenderer);
65
53
  return _super.apply(this, arguments);
66
54
  }
67
55
 
68
- (0, _createClass2.default)(ServerSideRenderer, [{
56
+ (0, _createClass2["default"])(ServerSideRenderer, [{
69
57
  key: "serializeArgsInClient",
70
58
  value:
71
59
  /**
@@ -76,7 +64,7 @@ var ServerSideRenderer = /*#__PURE__*/function (_RendererType) {
76
64
  * @returns the same object
77
65
  */
78
66
  function serializeArgsInClient(args) {
79
- return _objectSpread(_objectSpread({}, args), {}, {
67
+ return (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, args), {}, {
80
68
  config: (0, _mobxStateTree.isStateTreeNode)(args.config) ? (0, _mobxStateTree.getSnapshot)(args.config) : args.config,
81
69
  filters: args.filters && args.filters.toJSON().filters
82
70
  });
@@ -94,20 +82,20 @@ var ServerSideRenderer = /*#__PURE__*/function (_RendererType) {
94
82
  key: "deserializeResultsInClient",
95
83
  value: function deserializeResultsInClient(results, args) {
96
84
  var html = results.html,
97
- rest = (0, _objectWithoutProperties2.default)(results, _excluded); // if we are rendering svg, we skip hydration
85
+ rest = (0, _objectWithoutProperties2["default"])(results, _excluded); // if we are rendering svg, we skip hydration
98
86
 
99
87
  if (args.exportSVG) {
100
88
  // only return the results if the renderer explicitly has
101
89
  // this.supportsSVG support to avoid garbage being rendered in SVG
102
90
  // document
103
- return _objectSpread(_objectSpread({}, results), {}, {
91
+ return (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, results), {}, {
104
92
  html: this.supportsSVG ? results.html : '<text y="12" fill="black">SVG export not supported for this track</text>'
105
93
  });
106
94
  } // hydrate results using ServerSideRenderedContent
107
95
 
108
96
 
109
- return _objectSpread(_objectSpread({}, rest), {}, {
110
- reactElement: /*#__PURE__*/_react.default.createElement(_ServerSideRenderedContent.default, (0, _extends2.default)({}, args, results, {
97
+ return (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, rest), {}, {
98
+ reactElement: /*#__PURE__*/_react["default"].createElement(_ServerSideRenderedContent["default"], Object.assign({}, args, results, {
111
99
  RenderingComponent: this.ReactComponent
112
100
  }))
113
101
  });
@@ -122,13 +110,12 @@ var ServerSideRenderer = /*#__PURE__*/function (_RendererType) {
122
110
  }, {
123
111
  key: "deserializeArgsInWorker",
124
112
  value: function deserializeArgsInWorker(args) {
125
- var deserialized = _objectSpread({}, args);
126
-
113
+ var deserialized = (0, _objectSpread2["default"])({}, args);
127
114
  var config = this.configSchema.create(args.config || {}, {
128
115
  pluginManager: this.pluginManager
129
116
  });
130
117
  deserialized.config = config;
131
- deserialized.filters = new _serializableFilterChain.default({
118
+ deserialized.filters = new _serializableFilterChain["default"]({
132
119
  filters: args.filters
133
120
  });
134
121
  return deserialized;
@@ -145,11 +132,11 @@ var ServerSideRenderer = /*#__PURE__*/function (_RendererType) {
145
132
  }, {
146
133
  key: "serializeResultsInWorker",
147
134
  value: function serializeResultsInWorker(results, args) {
148
- var html = (0, _server.renderToString)( /*#__PURE__*/_react.default.createElement(_styles.ThemeProvider, {
135
+ var html = (0, _server.renderToString)( /*#__PURE__*/_react["default"].createElement(_styles.ThemeProvider, {
149
136
  theme: (0, _ui.createJBrowseTheme)(args.theme)
150
137
  }, results.reactElement));
151
138
  delete results.reactElement;
152
- return _objectSpread(_objectSpread({}, results), {}, {
139
+ return (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, results), {}, {
153
140
  html: html
154
141
  });
155
142
  }
@@ -164,8 +151,8 @@ var ServerSideRenderer = /*#__PURE__*/function (_RendererType) {
164
151
  }, {
165
152
  key: "renderInClient",
166
153
  value: function () {
167
- var _renderInClient = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(rpcManager, args) {
168
- return _regenerator.default.wrap(function _callee$(_context) {
154
+ var _renderInClient = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee(rpcManager, args) {
155
+ return _index["default"].wrap(function _callee$(_context) {
169
156
  while (1) {
170
157
  switch (_context.prev = _context.next) {
171
158
  case 0:
@@ -195,12 +182,12 @@ var ServerSideRenderer = /*#__PURE__*/function (_RendererType) {
195
182
  }, {
196
183
  key: "renderInWorker",
197
184
  value: function () {
198
- var _renderInWorker = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(args) {
185
+ var _renderInWorker = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee2(args) {
199
186
  var _this = this;
200
187
 
201
188
  var signal, _args$statusCallback, statusCallback, deserializedArgs, results, serialized;
202
189
 
203
- return _regenerator.default.wrap(function _callee2$(_context2) {
190
+ return _index["default"].wrap(function _callee2$(_context2) {
204
191
  while (1) {
205
192
  switch (_context2.prev = _context2.next) {
206
193
  case 0:
@@ -245,9 +232,9 @@ var ServerSideRenderer = /*#__PURE__*/function (_RendererType) {
245
232
  }, {
246
233
  key: "freeResourcesInClient",
247
234
  value: function () {
248
- var _freeResourcesInClient = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(rpcManager, args) {
235
+ var _freeResourcesInClient = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee3(rpcManager, args) {
249
236
  var serializedArgs, freed, freedRpc;
250
- return _regenerator.default.wrap(function _callee3$(_context3) {
237
+ return _index["default"].wrap(function _callee3$(_context3) {
251
238
  while (1) {
252
239
  switch (_context3.prev = _context3.next) {
253
240
  case 0:
@@ -276,6 +263,6 @@ var ServerSideRenderer = /*#__PURE__*/function (_RendererType) {
276
263
  }()
277
264
  }]);
278
265
  return ServerSideRenderer;
279
- }(_RendererType2.default);
266
+ }(_RendererType2["default"]);
280
267
 
281
- exports.default = ServerSideRenderer;
268
+ exports["default"] = ServerSideRenderer;
@@ -1,6 +1,6 @@
1
1
  "use strict";
2
2
 
3
- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
3
+ var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
4
4
 
5
5
  Object.defineProperty(exports, "__esModule", {
6
6
  value: true
@@ -8,43 +8,43 @@ Object.defineProperty(exports, "__esModule", {
8
8
  Object.defineProperty(exports, "BoxRendererType", {
9
9
  enumerable: true,
10
10
  get: function get() {
11
- return _BoxRendererType.default;
11
+ return _BoxRendererType["default"];
12
12
  }
13
13
  });
14
14
  Object.defineProperty(exports, "CircularChordRendererType", {
15
15
  enumerable: true,
16
16
  get: function get() {
17
- return _CircularChordRendererType.default;
17
+ return _CircularChordRendererType["default"];
18
18
  }
19
19
  });
20
20
  Object.defineProperty(exports, "ComparativeServerSideRendererType", {
21
21
  enumerable: true,
22
22
  get: function get() {
23
- return _ComparativeServerSideRendererType.default;
23
+ return _ComparativeServerSideRendererType["default"];
24
24
  }
25
25
  });
26
26
  Object.defineProperty(exports, "FeatureRendererType", {
27
27
  enumerable: true,
28
28
  get: function get() {
29
- return _FeatureRendererType.default;
29
+ return _FeatureRendererType["default"];
30
30
  }
31
31
  });
32
32
  Object.defineProperty(exports, "RendererType", {
33
33
  enumerable: true,
34
34
  get: function get() {
35
- return _RendererType.default;
35
+ return _RendererType["default"];
36
36
  }
37
37
  });
38
38
  Object.defineProperty(exports, "ServerSideRenderedContent", {
39
39
  enumerable: true,
40
40
  get: function get() {
41
- return _ServerSideRenderedContent.default;
41
+ return _ServerSideRenderedContent["default"];
42
42
  }
43
43
  });
44
44
  Object.defineProperty(exports, "ServerSideRendererType", {
45
45
  enumerable: true,
46
46
  get: function get() {
47
- return _ServerSideRendererType.default;
47
+ return _ServerSideRendererType["default"];
48
48
  }
49
49
  });
50
50
 
@@ -1,17 +1,15 @@
1
1
  "use strict";
2
2
 
3
- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
3
+ var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
4
4
 
5
5
  Object.defineProperty(exports, "__esModule", {
6
6
  value: true
7
7
  });
8
- exports.default = void 0;
8
+ exports["default"] = void 0;
9
9
 
10
- var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
10
+ var _classCallCheck2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/classCallCheck.js"));
11
11
 
12
- var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
13
-
14
- var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
12
+ var _createClass2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/createClass.js"));
15
13
 
16
14
  var _jexlStrings = require("../../../util/jexlStrings");
17
15
 
@@ -19,8 +17,8 @@ var SerializableFilterChain = /*#__PURE__*/function () {
19
17
  function SerializableFilterChain(_ref) {
20
18
  var _ref$filters = _ref.filters,
21
19
  filters = _ref$filters === void 0 ? [] : _ref$filters;
22
- (0, _classCallCheck2.default)(this, SerializableFilterChain);
23
- (0, _defineProperty2.default)(this, "filterChain", void 0);
20
+ (0, _classCallCheck2["default"])(this, SerializableFilterChain);
21
+ this.filterChain = void 0;
24
22
  this.filterChain = filters.map(function (inputFilter) {
25
23
  if (typeof inputFilter === 'string') {
26
24
  var expr = (0, _jexlStrings.stringToJexlExpression)(inputFilter);
@@ -35,7 +33,7 @@ var SerializableFilterChain = /*#__PURE__*/function () {
35
33
  } // eslint-disable-next-line @typescript-eslint/no-explicit-any
36
34
 
37
35
 
38
- (0, _createClass2.default)(SerializableFilterChain, [{
36
+ (0, _createClass2["default"])(SerializableFilterChain, [{
39
37
  key: "passes",
40
38
  value: function passes() {
41
39
  for (var i = 0; i < this.filterChain.length; i += 1) {
@@ -67,4 +65,4 @@ var SerializableFilterChain = /*#__PURE__*/function () {
67
65
  return SerializableFilterChain;
68
66
  }();
69
67
 
70
- exports.default = SerializableFilterChain;
68
+ exports["default"] = SerializableFilterChain;
@@ -1,11 +1,11 @@
1
1
  "use strict";
2
2
 
3
- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
3
+ var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
4
4
 
5
5
  var _serializableFilterChain = _interopRequireDefault(require("./serializableFilterChain"));
6
6
 
7
7
  test('one', function () {
8
- var c = new _serializableFilterChain.default({
8
+ var c = new _serializableFilterChain["default"]({
9
9
  filters: ["jexl:feature.y == 2"]
10
10
  });
11
11
  expect(c.passes({