npm - @jbrowse/plugin-data-management - Versions diffs - 2.1.7 → 2.2.1 - Mend

@jbrowse/plugin-data-management 2.1.7 → 2.2.1

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 (47) hide show

package/dist/AddConnectionWidget/components/ConfigureConnection.js CHANGED Viewed

@@ -24,12 +24,13 @@ var __importStar = (this && this.__importStar) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const plugin_config_1 = require("@jbrowse/plugin-config");
 const mobx_react_1 = require("mobx-react");
+const plugin_config_1 = require("@jbrowse/plugin-config");
+const ui_1 = require("@jbrowse/core/ui");
 const ConfigureConnection = (0, mobx_react_1.observer)((props) => {
     const { connectionType, model, session } = props;
     const ConfigEditorComponent = connectionType.configEditorComponent || plugin_config_1.ConfigurationEditor;
-    return (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null, "Loading...") },
+    return (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement(ui_1.LoadingEllipses, null) },
         react_1.default.createElement(ConfigEditorComponent, { model: { target: model }, session: session })));
 });
 exports.default = ConfigureConnection;

package/dist/AddConnectionWidget/components/ConfigureConnection.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"ConfigureConnection.js","sourceRoot":"","sources":["../../../src/AddConnectionWidget/components/ConfigureConnection.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,0DAA4D;~~AAC5D~~,~~2CAAqC~~;~~AAKrC~~,MAAM,mBAAmB,GAAG,IAAA,qBAAQ,EAClC,CAAC,KAIA,EAAE,EAAE;IACH,MAAM,EAAE,cAAc,EAAE,KAAK,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IAChD,MAAM,qBAAqB,GACzB,cAAc,CAAC,qBAAqB,IAAI,mCAAmB,CAAA;IAE7D,OAAO,CACL,8BAAC,gBAAQ,IAAC,QAAQ,EAAE,~~wDAAqB~~;~~QACvC~~,8BAAC,qBAAqB,IAAC,KAAK,EAAE,EAAE,MAAM,EAAE,KAAK,EAAE,EAAE,OAAO,EAAE,OAAO,GAAI,CAC5D,CACZ,CAAA;AACH,CAAC,CACF,CAAA;AAED,kBAAe,mBAAmB,CAAA"}
1	+ {"version":3,"file":"ConfigureConnection.js","sourceRoot":"","sources":["../../../src/AddConnectionWidget/components/ConfigureConnection.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,0DAA4D;AAI5D,yCAAkD;AAElD,MAAM,mBAAmB,GAAG,IAAA,qBAAQ,EAClC,CAAC,KAIA,EAAE,EAAE;IACH,MAAM,EAAE,cAAc,EAAE,KAAK,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IAChD,MAAM,qBAAqB,GACzB,cAAc,CAAC,qBAAqB,IAAI,mCAAmB,CAAA;IAE7D,OAAO,CACL,8BAAC,gBAAQ,IAAC,QAAQ,EAAE,8BAAC,oBAAe,OAAG;QACrC,8BAAC,qBAAqB,IAAC,KAAK,EAAE,EAAE,MAAM,EAAE,KAAK,EAAE,EAAE,OAAO,EAAE,OAAO,GAAI,CAC5D,CACZ,CAAA;AACH,CAAC,CACF,CAAA;AAED,kBAAe,mBAAmB,CAAA"}

package/dist/AddTrackWidget/components/AddTrackWidget.js CHANGED Viewed

@@ -8,12 +8,14 @@ const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
 const DefaultAddTrackWorkflow_1 = __importDefault(require("./DefaultAddTrackWorkflow"));
+const PasteConfigWorkflow_1 = __importDefault(require("./PasteConfigWorkflow"));
 function AddTrackSelector({ model }) {
     const [val, setVal] = (0, util_1.useLocalStorage)('trackSelector-choice', 'Default');
     const { pluginManager } = (0, util_1.getEnv)(model);
     const widgets = pluginManager.getElementTypesInGroup('add track workflow');
     const ComponentMap = {
         Default: DefaultAddTrackWorkflow_1.default,
+        'Add track JSON': PasteConfigWorkflow_1.default,
         ...Object.fromEntries(widgets.map(w => [w.name, w.ReactComponent])),
     };
     // make sure the selected value is in the list

package/dist/AddTrackWidget/components/AddTrackWidget.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"AddTrackWidget.js","sourceRoot":"","sources":["../../../src/AddTrackWidget/components/AddTrackWidget.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AACrC,4CAA6E;AAE7E,6CAA4D;AAI5D,wFAA+D;AAC/D,gFAAuD;AAEvD,SAAS,gBAAgB,CAAC,EAAE,KAAK,EAA4B;IAC3D,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,sBAAe,EAAC,sBAAsB,EAAE,SAAS,CAAC,CAAA;IACxE,MAAM,EAAE,aAAa,EAAE,GAAG,IAAA,aAAM,EAAC,KAAK,CAAC,CAAA;IACvC,MAAM,OAAO,GAAG,aAAa,CAAC,sBAAsB,CAClD,oBAAoB,CACK,CAAA;IAC3B,MAAM,YAAY,GAAG;QACnB,OAAO,EAAE,iCAAuB;QAChC,gBAAgB,EAAE,6BAAmB;QACrC,GAAG,MAAM,CAAC,WAAW,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC;KACX,CAAA;IAE1D,8CAA8C;IAC9C,MAAM,IAAI,GAAG,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CAAA;IAChD,MAAM,SAAS,GAAG,YAAY,CAAC,IAAI,CAAC,CAAA;IACpC,OAAO,CACL;QACE,8BAAC,sBAAW;YACV,8BAAC,iBAAM,IAAC,KAAK,EAAE,IAAI,EAAE,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,IAC/D,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAClC,8BAAC,mBAAQ,IAAC,GAAG,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,IACvB,CAAC,CACO,CACZ,CAAC,CACK;YACT,8BAAC,yBAAc,qCAA4C,CAC/C;QAEd,yCAAM;QACN,8BAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B,CACJ,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,gBAAgB,CAAC,CAAA"}

package/dist/AddTrackWidget/components/PasteConfigWorkflow.d.ts ADDED Viewed

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { AddTrackModel } from '../model';
+declare function AddTrackWorkflow({ model }: {
+    model: AddTrackModel;
+}): JSX.Element;
+declare const _default: typeof AddTrackWorkflow;
+export default _default;

package/dist/AddTrackWidget/components/PasteConfigWorkflow.js ADDED Viewed

@@ -0,0 +1,66 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importStar(require("react"));
+const material_1 = require("@mui/material");
+const ui_1 = require("@jbrowse/core/ui");
+const mui_1 = require("tss-react/mui");
+const util_1 = require("@jbrowse/core/util");
+const mobx_react_1 = require("mobx-react");
+const useStyles = (0, mui_1.makeStyles)()({
+    textbox: {
+        width: '100%',
+    },
+    submit: {
+        marginTop: 25,
+        marginBottom: 100,
+        display: 'block',
+    },
+});
+function AddTrackWorkflow({ model }) {
+    const { classes } = useStyles();
+    const [val, setVal] = (0, react_1.useState)('');
+    const [error, setError] = (0, react_1.useState)();
+    return (react_1.default.createElement("div", null,
+        error ? react_1.default.createElement(ui_1.ErrorMessage, { error: error }) : null,
+        react_1.default.createElement(material_1.TextField, { multiline: true, rows: 10, value: val, onChange: event => setVal(event.target.value), placeholder: 'Paste track config or array of track configs in JSON format', variant: "outlined", className: classes.textbox }),
+        react_1.default.createElement(material_1.Button, { variant: "contained", className: classes.submit, onClick: () => {
+                try {
+                    setError(undefined);
+                    const session = (0, util_1.getSession)(model);
+                    const conf = JSON.parse(val);
+                    const confs = Array.isArray(conf) ? conf : [conf];
+                    confs.forEach(c => session.addTrackConf(c));
+                    confs.forEach(c => c.trackId);
+                    model.clearData();
+                    session.hideWidget(model);
+                }
+                catch (e) {
+                    setError(e);
+                }
+            } }, "Submit")));
+}
+exports.default = (0, mobx_react_1.observer)(AddTrackWorkflow);
+//# sourceMappingURL=PasteConfigWorkflow.js.map

package/dist/AddTrackWidget/components/PasteConfigWorkflow.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"PasteConfigWorkflow.js","sourceRoot":"","sources":["../../../src/AddTrackWidget/components/PasteConfigWorkflow.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,4CAAiD;AACjD,yCAA+C;AAC/C,uCAA0C;AAC1C,6CAA+C;AAC/C,2CAAqC;AAKrC,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC;IAC7B,OAAO,EAAE;QACP,KAAK,EAAE,MAAM;KACd;IACD,MAAM,EAAE;QACN,SAAS,EAAE,EAAE;QACb,YAAY,EAAE,GAAG;QACjB,OAAO,EAAE,OAAO;KACjB;CACF,CAAC,CAAA;AAEF,SAAS,gBAAgB,CAAC,EAAE,KAAK,EAA4B;IAC3D,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,EAAE,CAAC,CAAA;IAClC,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,IAAA,gBAAQ,GAAW,CAAA;IAE7C,OAAO,CACL;QACG,KAAK,CAAC,CAAC,CAAC,8BAAC,iBAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;QAC9C,8BAAC,oBAAS,IACR,SAAS,QACT,IAAI,EAAE,EAAE,EACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,WAAW,EACT,6DAA6D,EAE/D,OAAO,EAAC,UAAU,EAClB,SAAS,EAAE,OAAO,CAAC,OAAO,GAC1B;QACF,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,SAAS,EAAE,OAAO,CAAC,MAAM,EACzB,OAAO,EAAE,GAAG,EAAE;gBACZ,IAAI;oBACF,QAAQ,CAAC,SAAS,CAAC,CAAA;oBACnB,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;oBACjC,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;oBAC5B,MAAM,KAAK,GAAG,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;oBACjD,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,CAAA;oBAC3C,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAA;oBAC7B,KAAK,CAAC,SAAS,EAAE,CAAA;oBACjB,OAAO,CAAC,UAAU,CAAC,KAAK,CAAC,CAAA;iBAC1B;gBAAC,OAAO,CAAC,EAAE;oBACV,QAAQ,CAAC,CAAC,CAAC,CAAA;iBACZ;YACH,CAAC,aAGM,CACL,CACP,CAAA;AACH,CAAC;AACD,kBAAe,IAAA,qBAAQ,EAAC,gBAAgB,CAAC,CAAA"}

package/dist/AddTrackWidget/model.d.ts CHANGED Viewed

@@ -46,6 +46,6 @@ export default function f(pluginManager: PluginManager): import("mobx-state-tree
 } & {
     readonly warningMessage: "" | "Warning: JBrowse cannot access files using the ftp protocol" | "Warning: one or more of your files do not provide the protocol e.g.\n          https://, please provide an absolute URL unless you are sure a\n          relative URL is intended." | "Warning: You entered a http:// resources but we cannot access HTTP\n          resources from JBrowse when it is running on https. Please use an\n          https URL for your track, or access the JBrowse app from the http\n          protocol";
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export declare type AddTrackStateModel = ReturnType<typeof f>;
-export declare type AddTrackModel = Instance<AddTrackStateModel>;
+export type AddTrackStateModel = ReturnType<typeof f>;
+export type AddTrackModel = Instance<AddTrackStateModel>;
 export {};

package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js CHANGED Viewed

@@ -146,7 +146,7 @@ const HierarchicalTrackSelector = (0, mobx_react_1.observer)(({ model, toolbarHe
     const [assemblyIdx, setAssemblyIdx] = (0, react_1.useState)(0);
     const [headerHeight, setHeaderHeight] = (0, react_1.useState)(0);
     const { assemblyNames } = model;
-    const assemblyName = assemblyNames[assemblyIdx];
+    const assemblyName = assemblyNames.length ? assemblyNames[assemblyIdx] : '';
     return assemblyName ? (react_1.default.createElement(react_1.default.Fragment, null,
         react_1.default.createElement(Header_1.default, { model: model, setHeaderHeight: setHeaderHeight, setAssemblyIdx: setAssemblyIdx, assemblyIdx: assemblyIdx }),
         react_1.default.createElement(AutoSizedHierarchicalTree, { tree: model.hierarchy(assemblyName), model: model, offset: toolbarHeight + headerHeight }))) : null;

package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/HierarchicalTrackSelectorWidget/model.d.ts CHANGED Viewed

@@ -1,7 +1,7 @@
 import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
-export declare type TreeNode = {
+export type TreeNode = {
     name: string;
     id: string;
     conf?: AnyConfigurationModel;
@@ -65,5 +65,5 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         tracks: AnyConfigurationModel[];
     }): TreeNode[];
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export declare type HierarchicalTrackSelectorStateModel = ReturnType<typeof stateTreeFactory>;
-export declare type HierarchicalTrackSelectorModel = Instance<HierarchicalTrackSelectorStateModel>;
+export type HierarchicalTrackSelectorStateModel = ReturnType<typeof stateTreeFactory>;
+export type HierarchicalTrackSelectorModel = Instance<HierarchicalTrackSelectorStateModel>;

package/dist/PluginStoreWidget/components/PluginStoreWidget.js CHANGED Viewed

@@ -27,10 +27,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const mobx_state_tree_1 = require("mobx-state-tree");
 const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
+const mobx_react_1 = require("mobx-react");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
 // icons
 const ExpandMore_1 = __importDefault(require("@mui/icons-material/ExpandMore"));
@@ -127,7 +128,7 @@ function PluginStoreWidget({ model }) {
                     .toLowerCase()
                     .includes(model.filterText.toLowerCase());
             })
-                .map(plugin => (react_1.default.createElement(PluginCard_1.default, { key: plugin.name, plugin: plugin, model: model, adminMode: !!adminMode })))) : (react_1.default.createElement(material_1.Typography, null, "Loading...")))));
+                .map(plugin => (react_1.default.createElement(PluginCard_1.default, { key: plugin.name, plugin: plugin, model: model, adminMode: !!adminMode })))) : (react_1.default.createElement(ui_1.LoadingEllipses, null)))));
 }
 exports.default = (0, mobx_react_1.observer)(PluginStoreWidget);
 //# sourceMappingURL=PluginStoreWidget.js.map

package/dist/PluginStoreWidget/components/PluginStoreWidget.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/PluginStoreWidget/model.d.ts CHANGED Viewed

@@ -9,5 +9,5 @@ export default function f(pluginManager: PluginManager): import("mobx-state-tree
     clearFilterText(): void;
     setFilterText(newText: string): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export declare type PluginStoreStateModel = ReturnType<typeof f>;
-export declare type PluginStoreModel = Instance<PluginStoreStateModel>;
+export type PluginStoreStateModel = ReturnType<typeof f>;
+export type PluginStoreModel = Instance<PluginStoreStateModel>;

package/dist/ucsc-trackhub/configSchema.d.ts CHANGED Viewed

@@ -1,2 +1,2 @@
-declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const UCSCTrackHubConnection: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default UCSCTrackHubConnection;

package/dist/ucsc-trackhub/configSchema.js CHANGED Viewed

@@ -2,7 +2,14 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 const configuration_1 = require("@jbrowse/core/configuration");
-exports.default = (0, configuration_1.ConfigurationSchema)('UCSCTrackHubConnection', {
+/**
+ * #config UCSCTrackHubConnection
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const UCSCTrackHubConnection = (0, configuration_1.ConfigurationSchema)('UCSCTrackHubConnection', {
+    /**
+     * #slot
+     */
     hubTxtLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -11,10 +18,19 @@ exports.default = (0, configuration_1.ConfigurationSchema)('UCSCTrackHubConnecti
         },
         description: 'location of the hub file (usually called hub.txt)',
     },
+    /**
+     * #slot
+     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
         description: 'optional list of genomes to import from this track hub, if empty all genomes will be imported',
     },
-}, { baseConfiguration: models_1.baseConnectionConfig });
+}, {
+    /**
+     * #baseConfiguration
+     */
+    baseConfiguration: models_1.baseConnectionConfig,
+});
+exports.default = UCSCTrackHubConnection;
 //# sourceMappingURL=configSchema.js.map

package/dist/ucsc-trackhub/configSchema.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/AddConnectionWidget/components/ConfigureConnection.js CHANGED Viewed

@@ -1,10 +1,11 @@
 import React, { Suspense } from 'react';
-import { ConfigurationEditor } from '@jbrowse/plugin-config';
 import { observer } from 'mobx-react';
+import { ConfigurationEditor } from '@jbrowse/plugin-config';
+import { LoadingEllipses } from '@jbrowse/core/ui';
 const ConfigureConnection = observer((props) => {
     const { connectionType, model, session } = props;
     const ConfigEditorComponent = connectionType.configEditorComponent || ConfigurationEditor;
-    return (React.createElement(Suspense, { fallback: React.createElement("div", null, "Loading...") },
+    return (React.createElement(Suspense, { fallback: React.createElement(LoadingEllipses, null) },
         React.createElement(ConfigEditorComponent, { model: { target: model }, session: session })));
 });
 export default ConfigureConnection;

package/esm/AddConnectionWidget/components/ConfigureConnection.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"ConfigureConnection.js","sourceRoot":"","sources":["../../../src/AddConnectionWidget/components/ConfigureConnection.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,mBAAmB,EAAE,MAAM,wBAAwB,CAAA;~~AAC5D~~,OAAO,EAAE,~~QAAQ~~,EAAE,MAAM,~~YAAY~~,CAAA;~~AAKrC~~,MAAM,mBAAmB,GAAG,QAAQ,CAClC,CAAC,KAIA,EAAE,EAAE;IACH,MAAM,EAAE,cAAc,EAAE,KAAK,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IAChD,MAAM,qBAAqB,GACzB,cAAc,CAAC,qBAAqB,IAAI,mBAAmB,CAAA;IAE7D,OAAO,CACL,oBAAC,QAAQ,IAAC,QAAQ,EAAE,~~8CAAqB~~;~~QACvC~~,oBAAC,qBAAqB,IAAC,KAAK,EAAE,EAAE,MAAM,EAAE,KAAK,EAAE,EAAE,OAAO,EAAE,OAAO,GAAI,CAC5D,CACZ,CAAA;AACH,CAAC,CACF,CAAA;AAED,eAAe,mBAAmB,CAAA"}
1	+ {"version":3,"file":"ConfigureConnection.js","sourceRoot":"","sources":["../../../src/AddConnectionWidget/components/ConfigureConnection.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,mBAAmB,EAAE,MAAM,wBAAwB,CAAA;AAI5D,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAElD,MAAM,mBAAmB,GAAG,QAAQ,CAClC,CAAC,KAIA,EAAE,EAAE;IACH,MAAM,EAAE,cAAc,EAAE,KAAK,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IAChD,MAAM,qBAAqB,GACzB,cAAc,CAAC,qBAAqB,IAAI,mBAAmB,CAAA;IAE7D,OAAO,CACL,oBAAC,QAAQ,IAAC,QAAQ,EAAE,oBAAC,eAAe,OAAG;QACrC,oBAAC,qBAAqB,IAAC,KAAK,EAAE,EAAE,MAAM,EAAE,KAAK,EAAE,EAAE,OAAO,EAAE,OAAO,GAAI,CAC5D,CACZ,CAAA;AACH,CAAC,CACF,CAAA;AAED,eAAe,mBAAmB,CAAA"}

package/esm/AddTrackWidget/components/AddTrackWidget.js CHANGED Viewed

@@ -3,12 +3,14 @@ import { observer } from 'mobx-react';
 import { FormControl, FormHelperText, Select, MenuItem } from '@mui/material';
 import { getEnv, useLocalStorage } from '@jbrowse/core/util';
 import DefaultAddTrackWorkflow from './DefaultAddTrackWorkflow';
+import PasteConfigWorkflow from './PasteConfigWorkflow';
 function AddTrackSelector({ model }) {
     const [val, setVal] = useLocalStorage('trackSelector-choice', 'Default');
     const { pluginManager } = getEnv(model);
     const widgets = pluginManager.getElementTypesInGroup('add track workflow');
     const ComponentMap = {
         Default: DefaultAddTrackWorkflow,
+        'Add track JSON': PasteConfigWorkflow,
         ...Object.fromEntries(widgets.map(w => [w.name, w.ReactComponent])),
     };
     // make sure the selected value is in the list

package/esm/AddTrackWidget/components/AddTrackWidget.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/AddTrackWidget/components/PasteConfigWorkflow.d.ts ADDED Viewed

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { AddTrackModel } from '../model';
+declare function AddTrackWorkflow({ model }: {
+    model: AddTrackModel;
+}): JSX.Element;
+declare const _default: typeof AddTrackWorkflow;
+export default _default;

package/esm/AddTrackWidget/components/PasteConfigWorkflow.js ADDED Viewed

@@ -0,0 +1,41 @@
+import React, { useState } from 'react';
+import { Button, TextField } from '@mui/material';
+import { ErrorMessage } from '@jbrowse/core/ui';
+import { makeStyles } from 'tss-react/mui';
+import { getSession } from '@jbrowse/core/util';
+import { observer } from 'mobx-react';
+const useStyles = makeStyles()({
+    textbox: {
+        width: '100%',
+    },
+    submit: {
+        marginTop: 25,
+        marginBottom: 100,
+        display: 'block',
+    },
+});
+function AddTrackWorkflow({ model }) {
+    const { classes } = useStyles();
+    const [val, setVal] = useState('');
+    const [error, setError] = useState();
+    return (React.createElement("div", null,
+        error ? React.createElement(ErrorMessage, { error: error }) : null,
+        React.createElement(TextField, { multiline: true, rows: 10, value: val, onChange: event => setVal(event.target.value), placeholder: 'Paste track config or array of track configs in JSON format', variant: "outlined", className: classes.textbox }),
+        React.createElement(Button, { variant: "contained", className: classes.submit, onClick: () => {
+                try {
+                    setError(undefined);
+                    const session = getSession(model);
+                    const conf = JSON.parse(val);
+                    const confs = Array.isArray(conf) ? conf : [conf];
+                    confs.forEach(c => session.addTrackConf(c));
+                    confs.forEach(c => c.trackId);
+                    model.clearData();
+                    session.hideWidget(model);
+                }
+                catch (e) {
+                    setError(e);
+                }
+            } }, "Submit")));
+}
+export default observer(AddTrackWorkflow);
+//# sourceMappingURL=PasteConfigWorkflow.js.map

package/esm/AddTrackWidget/components/PasteConfigWorkflow.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"PasteConfigWorkflow.js","sourceRoot":"","sources":["../../../src/AddTrackWidget/components/PasteConfigWorkflow.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AACjD,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAKrC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,OAAO,EAAE;QACP,KAAK,EAAE,MAAM;KACd;IACD,MAAM,EAAE;QACN,SAAS,EAAE,EAAE;QACb,YAAY,EAAE,GAAG;QACjB,OAAO,EAAE,OAAO;KACjB;CACF,CAAC,CAAA;AAEF,SAAS,gBAAgB,CAAC,EAAE,KAAK,EAA4B;IAC3D,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAClC,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAE7C,OAAO,CACL;QACG,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;QAC9C,oBAAC,SAAS,IACR,SAAS,QACT,IAAI,EAAE,EAAE,EACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,WAAW,EACT,6DAA6D,EAE/D,OAAO,EAAC,UAAU,EAClB,SAAS,EAAE,OAAO,CAAC,OAAO,GAC1B;QACF,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,SAAS,EAAE,OAAO,CAAC,MAAM,EACzB,OAAO,EAAE,GAAG,EAAE;gBACZ,IAAI;oBACF,QAAQ,CAAC,SAAS,CAAC,CAAA;oBACnB,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;oBACjC,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;oBAC5B,MAAM,KAAK,GAAG,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;oBACjD,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,CAAA;oBAC3C,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAA;oBAC7B,KAAK,CAAC,SAAS,EAAE,CAAA;oBACjB,OAAO,CAAC,UAAU,CAAC,KAAK,CAAC,CAAA;iBAC1B;gBAAC,OAAO,CAAC,EAAE;oBACV,QAAQ,CAAC,CAAC,CAAC,CAAA;iBACZ;YACH,CAAC,aAGM,CACL,CACP,CAAA;AACH,CAAC;AACD,eAAe,QAAQ,CAAC,gBAAgB,CAAC,CAAA"}

package/esm/AddTrackWidget/model.d.ts CHANGED Viewed

@@ -46,6 +46,6 @@ export default function f(pluginManager: PluginManager): import("mobx-state-tree
 } & {
     readonly warningMessage: "" | "Warning: JBrowse cannot access files using the ftp protocol" | "Warning: one or more of your files do not provide the protocol e.g.\n          https://, please provide an absolute URL unless you are sure a\n          relative URL is intended." | "Warning: You entered a http:// resources but we cannot access HTTP\n          resources from JBrowse when it is running on https. Please use an\n          https URL for your track, or access the JBrowse app from the http\n          protocol";
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export declare type AddTrackStateModel = ReturnType<typeof f>;
-export declare type AddTrackModel = Instance<AddTrackStateModel>;
+export type AddTrackStateModel = ReturnType<typeof f>;
+export type AddTrackModel = Instance<AddTrackStateModel>;
 export {};

package/esm/AddTrackWidget/model.js CHANGED Viewed

@@ -1,6 +1,6 @@
 import { types } from 'mobx-state-tree';
 import { ElementId } from '@jbrowse/core/util/types/mst';
-import { guessAdapter, guessTrackType, UNSUPPORTED, getFileName, } from '@jbrowse/core/util/tracks';
+import { guessAdapter, guessTrackType, getFileName, UNSUPPORTED, } from '@jbrowse/core/util/tracks';
 function isAbsoluteUrl(url = '') {
     try {
         new URL(url);

package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js CHANGED Viewed

@@ -118,7 +118,7 @@ const HierarchicalTrackSelector = observer(({ model, toolbarHeight = 0, }) => {
     const [assemblyIdx, setAssemblyIdx] = useState(0);
     const [headerHeight, setHeaderHeight] = useState(0);
     const { assemblyNames } = model;
-    const assemblyName = assemblyNames[assemblyIdx];
+    const assemblyName = assemblyNames.length ? assemblyNames[assemblyIdx] : '';
     return assemblyName ? (React.createElement(React.Fragment, null,
         React.createElement(Header, { model: model, setHeaderHeight: setHeaderHeight, setAssemblyIdx: setAssemblyIdx, assemblyIdx: assemblyIdx }),
         React.createElement(AutoSizedHierarchicalTree, { tree: model.hierarchy(assemblyName), model: model, offset: toolbarHeight + headerHeight }))) : null;

package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/HierarchicalTrackSelectorWidget/model.d.ts CHANGED Viewed

@@ -1,7 +1,7 @@
 import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
-export declare type TreeNode = {
+export type TreeNode = {
     name: string;
     id: string;
     conf?: AnyConfigurationModel;
@@ -65,5 +65,5 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         tracks: AnyConfigurationModel[];
     }): TreeNode[];
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export declare type HierarchicalTrackSelectorStateModel = ReturnType<typeof stateTreeFactory>;
-export declare type HierarchicalTrackSelectorModel = Instance<HierarchicalTrackSelectorStateModel>;
+export type HierarchicalTrackSelectorStateModel = ReturnType<typeof stateTreeFactory>;
+export type HierarchicalTrackSelectorModel = Instance<HierarchicalTrackSelectorStateModel>;

package/esm/PluginStoreWidget/components/PluginStoreWidget.js CHANGED Viewed

@@ -1,8 +1,9 @@
 import React, { useState, useEffect } from 'react';
-import { observer } from 'mobx-react';
-import { getEnv } from 'mobx-state-tree';
 import { Accordion, AccordionSummary, Button, IconButton, InputAdornment, TextField, Typography, } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
+import { observer } from 'mobx-react';
+import { getEnv } from 'mobx-state-tree';
+import { LoadingEllipses } from '@jbrowse/core/ui';
 import { getSession, isElectron } from '@jbrowse/core/util';
 // icons
 import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
@@ -99,7 +100,7 @@ function PluginStoreWidget({ model }) {
                     .toLowerCase()
                     .includes(model.filterText.toLowerCase());
             })
-                .map(plugin => (React.createElement(PluginCard, { key: plugin.name, plugin: plugin, model: model, adminMode: !!adminMode })))) : (React.createElement(Typography, null, "Loading...")))));
+                .map(plugin => (React.createElement(PluginCard, { key: plugin.name, plugin: plugin, model: model, adminMode: !!adminMode })))) : (React.createElement(LoadingEllipses, null)))));
 }
 export default observer(PluginStoreWidget);
 //# sourceMappingURL=PluginStoreWidget.js.map

package/esm/PluginStoreWidget/components/PluginStoreWidget.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/PluginStoreWidget/model.d.ts CHANGED Viewed

@@ -9,5 +9,5 @@ export default function f(pluginManager: PluginManager): import("mobx-state-tree
     clearFilterText(): void;
     setFilterText(newText: string): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export declare type PluginStoreStateModel = ReturnType<typeof f>;
-export declare type PluginStoreModel = Instance<PluginStoreStateModel>;
+export type PluginStoreStateModel = ReturnType<typeof f>;
+export type PluginStoreModel = Instance<PluginStoreStateModel>;

package/esm/ucsc-trackhub/configSchema.d.ts CHANGED Viewed

@@ -1,2 +1,2 @@
-declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const UCSCTrackHubConnection: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default UCSCTrackHubConnection;

package/esm/ucsc-trackhub/configSchema.js CHANGED Viewed

@@ -1,6 +1,13 @@
 import { baseConnectionConfig } from '@jbrowse/core/pluggableElementTypes/models';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-export default ConfigurationSchema('UCSCTrackHubConnection', {
+/**
+ * #config UCSCTrackHubConnection
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const UCSCTrackHubConnection = ConfigurationSchema('UCSCTrackHubConnection', {
+    /**
+     * #slot
+     */
     hubTxtLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -9,10 +16,19 @@ export default ConfigurationSchema('UCSCTrackHubConnection', {
         },
         description: 'location of the hub file (usually called hub.txt)',
     },
+    /**
+     * #slot
+     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
         description: 'optional list of genomes to import from this track hub, if empty all genomes will be imported',
     },
-}, { baseConfiguration: baseConnectionConfig });
+}, {
+    /**
+     * #baseConfiguration
+     */
+    baseConfiguration: baseConnectionConfig,
+});
+export default UCSCTrackHubConnection;
 //# sourceMappingURL=configSchema.js.map

package/esm/ucsc-trackhub/configSchema.js.map CHANGED Viewed

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