@jbrowse/core 1.7.11 → 2.1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/BaseFeatureWidget/BaseFeatureDetail.d.ts +20 -4
- package/BaseFeatureWidget/BaseFeatureDetail.js +313 -558
- package/BaseFeatureWidget/SequenceFeatureDetails.js +213 -473
- package/BaseFeatureWidget/index.d.ts +2 -2
- package/BaseFeatureWidget/index.js +88 -124
- package/BaseFeatureWidget/types.d.ts +1 -0
- package/BaseFeatureWidget/types.js +1 -4
- package/BaseFeatureWidget/util.js +40 -75
- package/CorePlugin.js +55 -94
- package/Plugin.js +9 -34
- package/PluginLoader.js +153 -422
- package/PluginManager.d.ts +84 -117
- package/PluginManager.js +377 -666
- package/ReExports/Attributes.d.ts +2 -0
- package/ReExports/Attributes.js +5 -0
- package/ReExports/BaseCard.d.ts +2 -0
- package/ReExports/BaseCard.js +5 -0
- package/ReExports/DataGrid.d.ts +2 -0
- package/ReExports/DataGrid.js +6 -0
- package/ReExports/FeatureDetails.d.ts +2 -0
- package/ReExports/FeatureDetails.js +5 -0
- package/ReExports/index.js +6 -12
- package/ReExports/list.d.ts +5 -0
- package/ReExports/list.js +271 -7
- package/ReExports/material-ui-colors.d.ts +1 -19
- package/ReExports/material-ui-colors.js +16 -158
- package/ReExports/modules.d.ts +68 -109
- package/ReExports/modules.js +455 -244
- package/TextSearch/BaseResults.js +51 -123
- package/TextSearch/TextSearchManager.d.ts +3 -1
- package/TextSearch/TextSearchManager.js +66 -144
- package/assemblyManager/assembly.js +280 -554
- package/assemblyManager/assemblyConfigSchema.js +47 -64
- package/assemblyManager/assemblyManager.d.ts +12 -10
- package/assemblyManager/assemblyManager.js +126 -270
- package/assemblyManager/index.js +9 -22
- package/configuration/configurationSchema.js +167 -203
- package/configuration/configurationSlot.js +248 -326
- package/configuration/index.js +19 -35
- package/configuration/util.d.ts +1 -1
- package/configuration/util.js +131 -173
- package/data_adapters/BaseAdapter.d.ts +2 -2
- package/data_adapters/BaseAdapter.js +132 -521
- package/data_adapters/CytobandAdapter.js +40 -126
- package/data_adapters/dataAdapterCache.js +77 -158
- package/package.json +16 -18
- package/pluggableElementTypes/AdapterType.js +24 -79
- package/pluggableElementTypes/AddTrackWorkflowType.d.ts +17 -0
- package/pluggableElementTypes/AddTrackWorkflowType.js +20 -0
- package/pluggableElementTypes/ConnectionType.js +22 -65
- package/pluggableElementTypes/DisplayType.js +35 -82
- package/pluggableElementTypes/InternetAccountType.js +23 -64
- package/pluggableElementTypes/PluggableElementBase.js +8 -20
- package/pluggableElementTypes/RpcMethodType.js +85 -427
- package/pluggableElementTypes/TextSearchAdapterType.js +16 -55
- package/pluggableElementTypes/TrackType.js +26 -70
- package/pluggableElementTypes/ViewType.js +21 -63
- package/pluggableElementTypes/WidgetType.js +21 -64
- package/pluggableElementTypes/index.d.ts +4 -3
- package/pluggableElementTypes/index.js +42 -125
- package/pluggableElementTypes/models/BaseConnectionModelFactory.js +28 -43
- package/pluggableElementTypes/models/BaseDisplayModel.d.ts +10 -10
- package/pluggableElementTypes/models/BaseDisplayModel.js +58 -95
- package/pluggableElementTypes/models/BaseTrackModel.d.ts +1 -1
- package/pluggableElementTypes/models/BaseTrackModel.js +139 -200
- package/pluggableElementTypes/models/BaseViewModel.js +24 -40
- package/pluggableElementTypes/models/InternetAccountModel.js +116 -263
- package/pluggableElementTypes/models/baseConnectionConfig.js +14 -25
- package/pluggableElementTypes/models/baseInternetAccountConfig.js +29 -38
- package/pluggableElementTypes/models/baseTrackConfig.js +106 -133
- package/pluggableElementTypes/models/index.js +21 -70
- package/pluggableElementTypes/renderers/BoxRendererType.js +132 -291
- package/pluggableElementTypes/renderers/CircularChordRendererType.js +8 -38
- package/pluggableElementTypes/renderers/ComparativeServerSideRendererType.js +60 -192
- package/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -2
- package/pluggableElementTypes/renderers/FeatureRendererType.js +89 -255
- package/pluggableElementTypes/renderers/RendererType.js +31 -105
- package/pluggableElementTypes/renderers/ServerSideRenderedContent.js +61 -72
- package/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +2 -2
- package/pluggableElementTypes/renderers/ServerSideRendererType.js +112 -265
- package/pluggableElementTypes/renderers/index.js +19 -62
- package/pluggableElementTypes/renderers/util/serializableFilterChain.js +27 -65
- package/rpc/BaseRpcDriver.js +169 -405
- package/rpc/MainThreadRpcDriver.js +27 -150
- package/rpc/RpcManager.js +58 -159
- package/rpc/WebWorkerRpcDriver.js +54 -171
- package/rpc/configSchema.js +25 -49
- package/rpc/coreRpcMethods.d.ts +1 -3
- package/rpc/coreRpcMethods.js +221 -959
- package/rpc/remoteAbortSignals.js +46 -70
- package/tsconfig.build.tsbuildinfo +1 -1
- package/ui/AboutDialog.js +107 -158
- package/ui/App.js +157 -261
- package/ui/AssemblySelector.d.ts +1 -1
- package/ui/AssemblySelector.js +59 -115
- package/ui/CascadingMenu.js +100 -199
- package/ui/ColorPicker.d.ts +16 -0
- package/ui/ColorPicker.js +97 -0
- package/ui/Drawer.js +28 -58
- package/ui/DrawerWidget.js +109 -209
- package/ui/DropDownMenu.d.ts +0 -8
- package/ui/DropDownMenu.js +60 -97
- package/ui/EditableTypography.d.ts +1 -1
- package/ui/EditableTypography.js +87 -155
- package/ui/ErrorMessage.js +41 -66
- package/ui/FactoryResetDialog.js +24 -57
- package/ui/FatalErrorDialog.js +59 -91
- package/ui/FileSelector/FileSelector.js +123 -189
- package/ui/FileSelector/LocalFileChooser.js +44 -71
- package/ui/FileSelector/UrlChooser.js +17 -38
- package/ui/FileSelector/index.js +6 -12
- package/ui/Icons.d.ts +1 -1
- package/ui/Icons.js +45 -69
- package/ui/Logo.js +57 -110
- package/ui/Menu.d.ts +1 -1
- package/ui/Menu.js +232 -355
- package/ui/PrerenderedCanvas.js +63 -78
- package/ui/ResizeHandle.js +87 -114
- package/ui/ReturnToImportFormDialog.js +32 -59
- package/ui/SanitizedHTML.js +63 -52
- package/ui/Snackbar.js +74 -99
- package/ui/SnackbarModel.js +37 -51
- package/ui/Tooltip.d.ts +3 -1
- package/ui/Tooltip.js +49 -74
- package/ui/ViewContainer.js +113 -183
- package/ui/colors.d.ts +10 -0
- package/ui/colors.js +78 -0
- package/ui/index.js +51 -181
- package/ui/react-colorful.d.ts +17 -0
- package/ui/react-colorful.js +455 -0
- package/ui/theme.d.ts +279 -131
- package/ui/theme.js +197 -225
- package/util/Base1DUtils.d.ts +32 -0
- package/util/Base1DUtils.js +174 -0
- package/util/Base1DViewModel.d.ts +16 -37
- package/util/Base1DViewModel.js +116 -295
- package/util/QuickLRU.js +84 -332
- package/util/TimeTraveller.d.ts +19 -0
- package/util/TimeTraveller.js +86 -0
- package/util/aborting.js +49 -127
- package/util/analytics.js +91 -154
- package/util/blockTypes.js +106 -240
- package/util/calculateDynamicBlocks.js +98 -128
- package/util/calculateStaticBlocks.js +105 -125
- package/util/color/cssColorsLevel4.js +156 -160
- package/util/color/index.js +33 -55
- package/util/compositeMap.js +49 -333
- package/util/formatFastaStrings.js +9 -14
- package/util/idMaker.js +18 -31
- package/util/index.d.ts +18 -39
- package/util/index.js +743 -1236
- package/util/io/RemoteFileWithRangeCache.js +88 -257
- package/util/io/index.js +95 -169
- package/util/jexl.js +60 -115
- package/util/jexlStrings.js +24 -29
- package/util/layouts/BaseLayout.js +1 -4
- package/util/layouts/GranularRectLayout.js +388 -557
- package/util/layouts/MultiLayout.js +41 -109
- package/util/layouts/PrecomputedLayout.js +56 -114
- package/util/layouts/PrecomputedMultiLayout.js +22 -59
- package/util/layouts/SceneGraph.js +127 -197
- package/util/layouts/index.js +29 -66
- package/util/mst-reflection.js +55 -71
- package/util/offscreenCanvasPonyfill.js +66 -134
- package/util/offscreenCanvasUtils.d.ts +2 -7
- package/util/offscreenCanvasUtils.js +49 -146
- package/util/range.js +29 -40
- package/util/rxjs.js +20 -27
- package/util/simpleFeature.js +88 -152
- package/util/stats.js +91 -151
- package/util/tracks.js +130 -171
- package/util/types/index.d.ts +3 -3
- package/util/types/index.js +110 -179
- package/util/types/mst.d.ts +3 -3
- package/util/types/mst.js +91 -142
- package/util/types/util.js +1 -4
- package/util/when.js +54 -101
- package/BaseFeatureWidget/SequenceFeatureDetails.test.js +0 -122
- package/BaseFeatureWidget/index.test.js +0 -51
- package/TextSearch/BaseResults.test.js +0 -42
- package/configuration/configurationSchema.test.js +0 -266
- package/configuration/configurationSlot.test.js +0 -69
- package/configuration/util.test.js +0 -39
- package/data_adapters/BaseAdapter.test.js +0 -200
- package/declare.d.js +0 -1
- package/pluggableElementTypes/RpcMethodType.test.js +0 -118
- package/pluggableElementTypes/renderers/declare.d.js +0 -1
- package/pluggableElementTypes/renderers/util/serializableFilterChain.test.js +0 -20
- package/rpc/BaseRpcDriver.test.js +0 -540
- package/rpc/declaration.d.js +0 -1
- package/ui/FatalErrorDialog.test.js +0 -82
- package/ui/SanitizedHTML.test.js +0 -36
- package/ui/theme.test.js +0 -111
- package/util/Base1DViewModel.test.js +0 -130
- package/util/calculateDynamicBlocks.test.js +0 -74
- package/util/calculateStaticBlocks.test.js +0 -297
- package/util/declare.d.js +0 -1
- package/util/formatFastaStrings.test.js +0 -40
- package/util/index.test.js +0 -213
- package/util/jexlStrings.test.js +0 -48
- package/util/layouts/GranularRectLayout.test.js +0 -99
- package/util/range.test.js +0 -64
- package/util/simpleFeature.test.js +0 -34
- package/util/stats.test.js +0 -172
package/ui/App.js
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react_1.default.createElement(session.DialogComponent, { ...session.DialogProps }))) : null,
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session.removeView(view);
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session.notify(`A view has been closed`, 'info', {
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});
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} },
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react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null, "Loading...") },
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react_1.default.createElement(ReactComponent, { model: view, session: session, getTrackType: pluginManager.getTrackType }))));
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})) : (react_1.default.createElement(material_1.Paper, { className: classes.selectPaper },
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react_1.default.createElement(material_1.Typography, null, "Select a view to launch"),
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react_1.default.createElement(material_1.Select, { value: value, onChange: event => setValue(event.target.value) }, viewTypes.map(({ name }) => (react_1.default.createElement(material_1.MenuItem, { key: name, value: name }, name)))),
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react_1.default.createElement(material_1.Button, { onClick: () => {
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session.addView(value, {});
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}, variant: "contained", color: "primary" }, "Launch view"))),
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react_1.default.createElement("div", { style: { height: 300 } }))),
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activeWidgets.size > 0 && minimized ? (react_1.default.createElement(material_1.Tooltip, { title: "Open drawer widget" },
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react_1.default.createElement(material_1.Fab, { className: drawerPosition === 'right' ? classes.fabRight : classes.fabLeft, color: "primary", "data-testid": "drawer-maximize", onClick: () => session.showWidgetDrawer() },
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react_1.default.createElement(Launch_1.default, null)))) : null,
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drawerVisible && drawerPosition === 'right' ? (react_1.default.createElement(DrawerWidget_1.default, { session: session })) : null,
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react_1.default.createElement(Snackbar_1.default, { session: session })));
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exports.default = App;
|
package/ui/AssemblySelector.d.ts
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|
/// <reference types="react" />
|
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|
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|
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|
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|
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|
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5
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|
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|
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CHANGED
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|
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|
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|
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if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|
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|
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|
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|
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|
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|
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|
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var useStyles = (0, _core.makeStyles)(function () {
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return {
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var __importStar = (this && this.__importStar) || function (mod) {
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if (mod && mod.__esModule) return mod;
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var result = {};
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if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
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__setModuleDefault(result, mod);
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return result;
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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const react_1 = __importStar(require("react"));
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const mobx_react_1 = require("mobx-react");
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const material_1 = require("@mui/material");
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const util_1 = require("@jbrowse/core/util");
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const mui_1 = require("tss-react/mui");
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// locals
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const configuration_1 = require("../configuration");
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const useStyles = (0, mui_1.makeStyles)()(() => ({
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importFormEntry: {
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function useLocalStorage(key, initialValue) {
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var _useState = (0, _react.useState)(function () {
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return initialValue;
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try {
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return item ? JSON.parse(item) : initialValue;
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console.error(error);
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return initialValue;
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}
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}),
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_useState2 = (0, _slicedToArray2.default)(_useState, 2),
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storedValue = _useState2[0],
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setStoredValue = _useState2[1];
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var setValue = function setValue(value) {
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try {
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setStoredValue(valueToStore);
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if (typeof window !== 'undefined') {
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window.localStorage.setItem(key, JSON.stringify(valueToStore));
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}
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} catch (error) {
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console.error(error);
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}
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};
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|
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return [storedValue, setValue];
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|
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}
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67
|
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68
|
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var AssemblySelector = (0, _mobxReact.observer)(function (_ref) {
|
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69
|
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var session = _ref.session,
|
|
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|
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onChange = _ref.onChange,
|
|
71
|
-
selected = _ref.selected,
|
|
72
|
-
InputProps = _ref.InputProps,
|
|
73
|
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_ref$extra = _ref.extra,
|
|
74
|
-
extra = _ref$extra === void 0 ? 0 : _ref$extra;
|
|
75
|
-
var classes = useStyles();
|
|
76
|
-
var assemblyNames = session.assemblyNames,
|
|
77
|
-
assemblyManager = session.assemblyManager; // constructs a localstorage key based on host/path/config to help
|
|
78
|
-
// remember. non-config assists usage with e.g. embedded apps
|
|
79
|
-
|
|
80
|
-
var config = new URLSearchParams(window.location.search).get('config');
|
|
81
|
-
|
|
82
|
-
var _useLocalStorage = useLocalStorage("lastAssembly-".concat([window.location.host + window.location.pathname, config, extra].join('-')), selected),
|
|
83
|
-
_useLocalStorage2 = (0, _slicedToArray2.default)(_useLocalStorage, 2),
|
|
84
|
-
lastSelected = _useLocalStorage2[0],
|
|
85
|
-
setLastSelected = _useLocalStorage2[1];
|
|
86
|
-
|
|
87
|
-
var selection = assemblyNames.includes(lastSelected || '') ? lastSelected : selected;
|
|
88
|
-
(0, _react.useEffect)(function () {
|
|
89
|
-
if (selection && selection !== selected) {
|
|
90
|
-
onChange(selection);
|
|
91
|
-
}
|
|
92
|
-
}, [selection, onChange, selected]);
|
|
93
|
-
var error = assemblyNames.length ? '' : 'No configured assemblies';
|
|
94
|
-
return /*#__PURE__*/_react.default.createElement(_core.TextField, {
|
|
95
|
-
select: true,
|
|
96
|
-
label: "Assembly",
|
|
97
|
-
variant: "outlined",
|
|
98
|
-
helperText: error || 'Select assembly to view',
|
|
99
|
-
value: error ? '' : selection,
|
|
100
|
-
inputProps: {
|
|
101
|
-
'data-testid': 'assembly-selector'
|
|
102
|
-
},
|
|
103
|
-
onChange: function onChange(event) {
|
|
104
|
-
return setLastSelected(event.target.value);
|
|
35
|
+
minWidth: 180,
|
|
105
36
|
},
|
|
106
|
-
|
|
107
|
-
|
|
108
|
-
|
|
109
|
-
|
|
110
|
-
|
|
111
|
-
|
|
112
|
-
|
|
113
|
-
|
|
114
|
-
|
|
115
|
-
|
|
116
|
-
|
|
117
|
-
|
|
37
|
+
}));
|
|
38
|
+
const AssemblySelector = (0, mobx_react_1.observer)(({ session, onChange, selected, InputProps, extra = 0, }) => {
|
|
39
|
+
const { classes } = useStyles();
|
|
40
|
+
const { assemblyNames, assemblyManager } = session;
|
|
41
|
+
// constructs a localstorage key based on host/path/config to help
|
|
42
|
+
// remember. non-config assists usage with e.g. embedded apps
|
|
43
|
+
const config = new URLSearchParams(window.location.search).get('config');
|
|
44
|
+
const [lastSelected, setLastSelected] = (0, util_1.useLocalStorage)(`lastAssembly-${[
|
|
45
|
+
window.location.host + window.location.pathname,
|
|
46
|
+
config,
|
|
47
|
+
extra,
|
|
48
|
+
].join('-')}`, selected);
|
|
49
|
+
const selection = assemblyNames.includes(lastSelected || '')
|
|
50
|
+
? lastSelected
|
|
51
|
+
: selected;
|
|
52
|
+
(0, react_1.useEffect)(() => {
|
|
53
|
+
if (selection && selection !== selected) {
|
|
54
|
+
onChange(selection);
|
|
55
|
+
}
|
|
56
|
+
}, [selection, onChange, selected]);
|
|
57
|
+
const error = assemblyNames.length ? '' : 'No configured assemblies';
|
|
58
|
+
return (react_1.default.createElement(material_1.TextField, { select: true, label: "Assembly", variant: "outlined", helperText: error || 'Select assembly to view', value: error ? '' : selection, inputProps: { 'data-testid': 'assembly-selector' }, onChange: event => setLastSelected(event.target.value), error: !!error, InputProps: InputProps, disabled: !!error, className: classes.importFormEntry }, assemblyNames.map(name => {
|
|
59
|
+
const assembly = assemblyManager.get(name);
|
|
60
|
+
const displayName = assembly ? (0, configuration_1.getConf)(assembly, 'displayName') : '';
|
|
61
|
+
return (react_1.default.createElement(material_1.MenuItem, { key: name, value: name }, displayName || name));
|
|
62
|
+
})));
|
|
118
63
|
});
|
|
119
|
-
|
|
120
|
-
exports.default = _default;
|
|
64
|
+
exports.default = AssemblySelector;
|