@jbrowse/core 1.5.6 → 1.6.0

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Files changed (155) hide show
  1. package/BaseFeatureWidget/BaseFeatureDetail.js +91 -78
  2. package/BaseFeatureWidget/SequenceFeatureDetails.js +65 -57
  3. package/BaseFeatureWidget/SequenceFeatureDetails.test.js +9 -9
  4. package/BaseFeatureWidget/index.js +1 -1
  5. package/BaseFeatureWidget/index.test.js +4 -4
  6. package/BaseFeatureWidget/util.js +13 -9
  7. package/CorePlugin.js +32 -20
  8. package/Plugin.js +13 -11
  9. package/PluginLoader.js +38 -33
  10. package/PluginManager.d.ts +8 -5
  11. package/PluginManager.js +142 -53
  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.d.ts +7 -5
  16. package/ReExports/modules.js +51 -47
  17. package/TextSearch/BaseResults.js +34 -24
  18. package/TextSearch/BaseResults.test.js +7 -3
  19. package/TextSearch/TextSearchManager.js +17 -15
  20. package/assemblyManager/assembly.js +39 -34
  21. package/assemblyManager/assemblyConfigSchema.js +2 -2
  22. package/assemblyManager/assemblyManager.js +20 -16
  23. package/assemblyManager/index.js +3 -3
  24. package/babel.config.d.ts +15 -0
  25. package/babel.config.js +19 -0
  26. package/configuration/configurationSchema.js +19 -17
  27. package/configuration/configurationSlot.js +11 -11
  28. package/configuration/configurationSlot.test.js +5 -5
  29. package/configuration/index.d.ts +1 -0
  30. package/configuration/util.js +5 -5
  31. package/data_adapters/BaseAdapter.d.ts +15 -3
  32. package/data_adapters/BaseAdapter.js +216 -62
  33. package/data_adapters/BaseAdapter.test.js +30 -24
  34. package/data_adapters/CytobandAdapter.d.ts +1 -1
  35. package/data_adapters/CytobandAdapter.js +25 -19
  36. package/data_adapters/dataAdapterCache.js +9 -9
  37. package/package.json +4 -5
  38. package/pluggableElementTypes/AdapterType.js +31 -22
  39. package/pluggableElementTypes/ConnectionType.js +28 -18
  40. package/pluggableElementTypes/DisplayType.js +27 -17
  41. package/pluggableElementTypes/InternetAccountType.js +24 -14
  42. package/pluggableElementTypes/PluggableElementBase.js +10 -8
  43. package/pluggableElementTypes/RpcMethodType.d.ts +1 -1
  44. package/pluggableElementTypes/RpcMethodType.js +141 -118
  45. package/pluggableElementTypes/RpcMethodType.test.js +23 -17
  46. package/pluggableElementTypes/TextSearchAdapterType.js +25 -15
  47. package/pluggableElementTypes/TrackType.js +25 -15
  48. package/pluggableElementTypes/ViewType.js +25 -15
  49. package/pluggableElementTypes/WidgetType.js +27 -17
  50. package/pluggableElementTypes/index.js +11 -11
  51. package/pluggableElementTypes/models/BaseConnectionModelFactory.js +5 -5
  52. package/pluggableElementTypes/models/BaseDisplayModel.js +8 -5
  53. package/pluggableElementTypes/models/BaseTrackModel.js +11 -8
  54. package/pluggableElementTypes/models/BaseViewModel.js +3 -3
  55. package/pluggableElementTypes/models/InternetAccountModel.d.ts +1 -1
  56. package/pluggableElementTypes/models/InternetAccountModel.js +5 -5
  57. package/pluggableElementTypes/models/baseConnectionConfig.js +2 -2
  58. package/pluggableElementTypes/models/baseTrackConfig.js +7 -4
  59. package/pluggableElementTypes/models/index.js +4 -4
  60. package/pluggableElementTypes/renderers/BoxRendererType.js +49 -39
  61. package/pluggableElementTypes/renderers/CircularChordRendererType.js +18 -12
  62. package/pluggableElementTypes/renderers/ComparativeServerSideRendererType.js +35 -27
  63. package/pluggableElementTypes/renderers/FeatureRendererType.js +46 -36
  64. package/pluggableElementTypes/renderers/RendererType.js +31 -21
  65. package/pluggableElementTypes/renderers/ServerSideRenderedContent.js +12 -8
  66. package/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +1 -1
  67. package/pluggableElementTypes/renderers/ServerSideRendererType.js +45 -33
  68. package/pluggableElementTypes/renderers/index.js +8 -8
  69. package/pluggableElementTypes/renderers/util/serializableFilterChain.js +10 -8
  70. package/pluggableElementTypes/renderers/util/serializableFilterChain.test.js +2 -2
  71. package/rpc/BaseRpcDriver.js +43 -38
  72. package/rpc/BaseRpcDriver.test.js +63 -49
  73. package/rpc/MainThreadRpcDriver.js +32 -22
  74. package/rpc/RpcManager.js +19 -17
  75. package/rpc/WebWorkerRpcDriver.js +38 -28
  76. package/rpc/configSchema.js +2 -2
  77. package/rpc/coreRpcMethods.d.ts +16 -0
  78. package/rpc/coreRpcMethods.js +248 -121
  79. package/rpc/remoteAbortSignals.js +3 -3
  80. package/ui/AboutDialog.js +21 -17
  81. package/ui/App.js +42 -38
  82. package/ui/AssemblySelector.d.ts +1 -1
  83. package/ui/AssemblySelector.js +6 -6
  84. package/ui/Drawer.js +7 -7
  85. package/ui/DrawerWidget.d.ts +1 -1
  86. package/ui/DrawerWidget.js +37 -33
  87. package/ui/DropDownMenu.js +21 -9
  88. package/ui/EditableTypography.js +30 -19
  89. package/ui/ErrorMessage.js +5 -5
  90. package/ui/FactoryResetDialog.js +8 -8
  91. package/ui/FatalErrorDialog.js +29 -12
  92. package/ui/FatalErrorDialog.test.js +11 -11
  93. package/ui/FileSelector/FileSelector.js +42 -32
  94. package/ui/FileSelector/LocalFileChooser.js +9 -9
  95. package/ui/FileSelector/UrlChooser.js +4 -4
  96. package/ui/FileSelector/index.js +4 -4
  97. package/ui/Icons.js +9 -9
  98. package/ui/Logo.js +19 -19
  99. package/ui/Menu.js +46 -35
  100. package/ui/NewSessionCards.js +29 -19
  101. package/ui/PrerenderedCanvas.js +27 -10
  102. package/ui/ResizeHandle.js +17 -10
  103. package/ui/SanitizedHTML.js +5 -5
  104. package/ui/SanitizedHTML.test.js +4 -4
  105. package/ui/Snackbar.js +16 -12
  106. package/ui/SnackbarModel.js +1 -1
  107. package/ui/Tooltip.js +11 -7
  108. package/ui/ViewContainer.d.ts +2 -5
  109. package/ui/ViewContainer.js +44 -49
  110. package/ui/index.d.ts +1 -0
  111. package/ui/index.js +26 -13
  112. package/ui/theme.js +15 -11
  113. package/util/Base1DViewModel.d.ts +14 -12
  114. package/util/Base1DViewModel.js +51 -55
  115. package/util/Base1DViewModel.test.js +5 -5
  116. package/util/QuickLRU.js +31 -27
  117. package/util/aborting.js +26 -16
  118. package/util/analytics.d.ts +1 -0
  119. package/util/analytics.js +15 -7
  120. package/util/blockTypes.js +48 -36
  121. package/util/calculateDynamicBlocks.js +4 -4
  122. package/util/calculateDynamicBlocks.test.js +14 -10
  123. package/util/calculateStaticBlocks.js +1 -1
  124. package/util/calculateStaticBlocks.test.js +15 -15
  125. package/util/compositeMap.js +31 -27
  126. package/util/idMaker.js +4 -4
  127. package/util/index.d.ts +23 -1
  128. package/util/index.js +133 -39
  129. package/util/index.test.js +11 -7
  130. package/util/io/RemoteFileWithRangeCache.js +41 -29
  131. package/util/io/index.js +6 -6
  132. package/util/jexl.js +5 -5
  133. package/util/jexlStrings.js +2 -2
  134. package/util/jexlStrings.test.js +2 -2
  135. package/util/layouts/GranularRectLayout.js +33 -27
  136. package/util/layouts/GranularRectLayout.test.js +10 -10
  137. package/util/layouts/MultiLayout.js +19 -13
  138. package/util/layouts/PrecomputedLayout.js +16 -14
  139. package/util/layouts/PrecomputedMultiLayout.js +23 -17
  140. package/util/layouts/SceneGraph.js +18 -12
  141. package/util/layouts/index.js +6 -6
  142. package/util/offscreenCanvasPonyfill.js +31 -29
  143. package/util/offscreenCanvasUtils.js +6 -6
  144. package/util/range.test.js +20 -20
  145. package/util/rxjs.js +2 -2
  146. package/util/simpleFeature.js +23 -18
  147. package/util/simpleFeature.test.js +3 -3
  148. package/util/stats.d.ts +1 -1
  149. package/util/stats.js +11 -7
  150. package/util/stats.test.js +16 -16
  151. package/util/tracks.js +1 -3
  152. package/util/types/index.d.ts +1 -1
  153. package/util/types/index.js +36 -31
  154. package/util/types/mst.js +19 -15
  155. package/util/when.js +6 -6
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+
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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; }
53
+
54
+ function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
55
+
56
+ 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; } }
57
+
46
58
  var ServerSideRenderer = /*#__PURE__*/function (_RendererType) {
47
- (0, _inherits2["default"])(ServerSideRenderer, _RendererType);
59
+ (0, _inherits2.default)(ServerSideRenderer, _RendererType);
48
60
 
49
- var _super = (0, _createSuper2["default"])(ServerSideRenderer);
61
+ var _super = _createSuper(ServerSideRenderer);
50
62
 
51
63
  function ServerSideRenderer() {
52
- (0, _classCallCheck2["default"])(this, ServerSideRenderer);
64
+ (0, _classCallCheck2.default)(this, ServerSideRenderer);
53
65
  return _super.apply(this, arguments);
54
66
  }
55
67
 
56
- (0, _createClass2["default"])(ServerSideRenderer, [{
68
+ (0, _createClass2.default)(ServerSideRenderer, [{
57
69
  key: "serializeArgsInClient",
58
70
  value:
59
71
  /**
@@ -64,7 +76,7 @@ var ServerSideRenderer = /*#__PURE__*/function (_RendererType) {
64
76
  * @returns the same object
65
77
  */
66
78
  function serializeArgsInClient(args) {
67
- return (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, args), {}, {
79
+ return _objectSpread(_objectSpread({}, args), {}, {
68
80
  config: (0, _mobxStateTree.isStateTreeNode)(args.config) ? (0, _mobxStateTree.getSnapshot)(args.config) : args.config,
69
81
  filters: args.filters && args.filters.toJSON().filters
70
82
  });
@@ -82,20 +94,20 @@ var ServerSideRenderer = /*#__PURE__*/function (_RendererType) {
82
94
  key: "deserializeResultsInClient",
83
95
  value: function deserializeResultsInClient(results, args) {
84
96
  var html = results.html,
85
- rest = (0, _objectWithoutProperties2["default"])(results, _excluded); // if we are rendering svg, we skip hydration
97
+ rest = (0, _objectWithoutProperties2.default)(results, _excluded); // if we are rendering svg, we skip hydration
86
98
 
87
99
  if (args.exportSVG) {
88
100
  // only return the results if the renderer explicitly has
89
101
  // this.supportsSVG support to avoid garbage being rendered in SVG
90
102
  // document
91
- return (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, results), {}, {
103
+ return _objectSpread(_objectSpread({}, results), {}, {
92
104
  html: this.supportsSVG ? results.html : '<text y="12" fill="black">SVG export not supported for this track</text>'
93
105
  });
94
106
  } // hydrate results using ServerSideRenderedContent
95
107
 
96
108
 
97
- return (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, rest), {}, {
98
- reactElement: /*#__PURE__*/_react["default"].createElement(_ServerSideRenderedContent["default"], Object.assign({}, args, results, {
109
+ return _objectSpread(_objectSpread({}, rest), {}, {
110
+ reactElement: /*#__PURE__*/_react.default.createElement(_ServerSideRenderedContent.default, (0, _extends2.default)({}, args, results, {
99
111
  RenderingComponent: this.ReactComponent
100
112
  }))
101
113
  });
@@ -110,12 +122,12 @@ var ServerSideRenderer = /*#__PURE__*/function (_RendererType) {
110
122
  }, {
111
123
  key: "deserializeArgsInWorker",
112
124
  value: function deserializeArgsInWorker(args) {
113
- var deserialized = (0, _objectSpread2["default"])({}, args);
114
- var config = this.configSchema.create(args.config || {}, {
125
+ var deserialized = _objectSpread({}, args);
126
+
127
+ deserialized.config = this.configSchema.create(args.config || {}, {
115
128
  pluginManager: this.pluginManager
116
129
  });
117
- deserialized.config = config;
118
- deserialized.filters = new _serializableFilterChain["default"]({
130
+ deserialized.filters = new _serializableFilterChain.default({
119
131
  filters: args.filters
120
132
  });
121
133
  return deserialized;
@@ -132,11 +144,11 @@ var ServerSideRenderer = /*#__PURE__*/function (_RendererType) {
132
144
  }, {
133
145
  key: "serializeResultsInWorker",
134
146
  value: function serializeResultsInWorker(results, args) {
135
- var html = (0, _server.renderToString)( /*#__PURE__*/_react["default"].createElement(_styles.ThemeProvider, {
147
+ var html = (0, _server.renderToString)( /*#__PURE__*/_react.default.createElement(_styles.ThemeProvider, {
136
148
  theme: (0, _ui.createJBrowseTheme)(args.theme)
137
149
  }, results.reactElement));
138
150
  delete results.reactElement;
139
- return (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, results), {}, {
151
+ return _objectSpread(_objectSpread({}, results), {}, {
140
152
  html: html
141
153
  });
142
154
  }
@@ -151,8 +163,8 @@ var ServerSideRenderer = /*#__PURE__*/function (_RendererType) {
151
163
  }, {
152
164
  key: "renderInClient",
153
165
  value: function () {
154
- var _renderInClient = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee(rpcManager, args) {
155
- return _index["default"].wrap(function _callee$(_context) {
166
+ var _renderInClient = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(rpcManager, args) {
167
+ return _regenerator.default.wrap(function _callee$(_context) {
156
168
  while (1) {
157
169
  switch (_context.prev = _context.next) {
158
170
  case 0:
@@ -182,12 +194,12 @@ var ServerSideRenderer = /*#__PURE__*/function (_RendererType) {
182
194
  }, {
183
195
  key: "renderInWorker",
184
196
  value: function () {
185
- var _renderInWorker = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee2(args) {
197
+ var _renderInWorker = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(args) {
186
198
  var _this = this;
187
199
 
188
200
  var signal, _args$statusCallback, statusCallback, deserializedArgs, results, serialized;
189
201
 
190
- return _index["default"].wrap(function _callee2$(_context2) {
202
+ return _regenerator.default.wrap(function _callee2$(_context2) {
191
203
  while (1) {
192
204
  switch (_context2.prev = _context2.next) {
193
205
  case 0:
@@ -232,9 +244,9 @@ var ServerSideRenderer = /*#__PURE__*/function (_RendererType) {
232
244
  }, {
233
245
  key: "freeResourcesInClient",
234
246
  value: function () {
235
- var _freeResourcesInClient = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee3(rpcManager, args) {
247
+ var _freeResourcesInClient = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(rpcManager, args) {
236
248
  var serializedArgs, freed, freedRpc;
237
- return _index["default"].wrap(function _callee3$(_context3) {
249
+ return _regenerator.default.wrap(function _callee3$(_context3) {
238
250
  while (1) {
239
251
  switch (_context3.prev = _context3.next) {
240
252
  case 0:
@@ -263,6 +275,6 @@ var ServerSideRenderer = /*#__PURE__*/function (_RendererType) {
263
275
  }()
264
276
  }]);
265
277
  return ServerSideRenderer;
266
- }(_RendererType2["default"]);
278
+ }(_RendererType2.default);
267
279
 
268
- exports["default"] = ServerSideRenderer;
280
+ exports.default = ServerSideRenderer;
@@ -1,6 +1,6 @@
1
1
  "use strict";
2
2
 
3
- var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
3
+ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
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
 
@@ -1,15 +1,17 @@
1
1
  "use strict";
2
2
 
3
- var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
3
+ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
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("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/classCallCheck.js"));
10
+ var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
11
11
 
12
- var _createClass2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/createClass.js"));
12
+ var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
13
+
14
+ var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
13
15
 
14
16
  var _jexlStrings = require("../../../util/jexlStrings");
15
17
 
@@ -17,8 +19,8 @@ var SerializableFilterChain = /*#__PURE__*/function () {
17
19
  function SerializableFilterChain(_ref) {
18
20
  var _ref$filters = _ref.filters,
19
21
  filters = _ref$filters === void 0 ? [] : _ref$filters;
20
- (0, _classCallCheck2["default"])(this, SerializableFilterChain);
21
- this.filterChain = void 0;
22
+ (0, _classCallCheck2.default)(this, SerializableFilterChain);
23
+ (0, _defineProperty2.default)(this, "filterChain", void 0);
22
24
  this.filterChain = filters.map(function (inputFilter) {
23
25
  if (typeof inputFilter === 'string') {
24
26
  var expr = (0, _jexlStrings.stringToJexlExpression)(inputFilter);
@@ -33,7 +35,7 @@ var SerializableFilterChain = /*#__PURE__*/function () {
33
35
  } // eslint-disable-next-line @typescript-eslint/no-explicit-any
34
36
 
35
37
 
36
- (0, _createClass2["default"])(SerializableFilterChain, [{
38
+ (0, _createClass2.default)(SerializableFilterChain, [{
37
39
  key: "passes",
38
40
  value: function passes() {
39
41
  for (var i = 0; i < this.filterChain.length; i += 1) {
@@ -65,4 +67,4 @@ var SerializableFilterChain = /*#__PURE__*/function () {
65
67
  return SerializableFilterChain;
66
68
  }();
67
69
 
68
- exports["default"] = SerializableFilterChain;
70
+ exports.default = SerializableFilterChain;
@@ -1,11 +1,11 @@
1
1
  "use strict";
2
2
 
3
- var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
3
+ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
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({