@jbrowse/plugin-data-management 2.4.2 → 2.6.1

package/dist/HierarchicalTrackSelectorWidget/components/tree/HierarchicalTree.d.ts

@@ -1,8 +1,8 @@
-/// <reference types="react" />
+import React from 'react';
 import { TreeNode, HierarchicalTrackSelectorModel } from '../../model';
 declare const _default: ({ height, tree, model, }: {
     height: number;
     tree: TreeNode;
     model: HierarchicalTrackSelectorModel;
-}) => JSX.Element;
+}) => React.JSX.Element;
 export default _default;

package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackCategory.d.ts

@@ -1,7 +1,7 @@
-/// <reference types="react" />
+import React from 'react';
 import { NodeData } from '../util';
 export default function Category({ isOpen, setOpen, data, }: {
     isOpen: boolean;
     setOpen: (arg: boolean) => void;
     data: NodeData;
-}): JSX.Element;
+}): React.JSX.Element;

package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackLabel.d.ts

@@ -1,4 +1,4 @@
-/// <reference types="react" />
+import React from 'react';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { NodeData } from '../util';
 export interface InfoArgs {
@@ -8,4 +8,4 @@ export interface InfoArgs {
 }
 export default function TrackLabel({ data }: {
     data: NodeData;
-}): JSX.Element;
+}): React.JSX.Element;

package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackListNode.d.ts

@@ -1,4 +1,4 @@
-/// <reference types="react" />
+import React from 'react';
 import { NodeData } from '../util';
 export default function Node({ data, isOpen, style, setOpen, }: {
     data: NodeData;
@@ -7,4 +7,4 @@ export default function Node({ data, isOpen, style, setOpen, }: {
         height: number;
     };
     setOpen: (arg: boolean) => void;
-}): JSX.Element;
+}): React.JSX.Element;

package/dist/HierarchicalTrackSelectorWidget/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/dist/HierarchicalTrackSelectorWidget/model.d.ts

@@ -14,10 +14,25 @@ export type TreeNode = {
 export declare function generateHierarchy(model: HierarchicalTrackSelectorModel, trackConfigurations: AnyConfigurationModel[], collapsed: {
     get: (arg: string) => boolean | undefined;
 }, extra?: string): TreeNode[];
+/**
+ * #stateModel HierarchicalTrackSelectorWidget
+ */
 export default function stateTreeFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
+    /**
+     * #property
+     */
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    /**
+     * #property
+     */
     type: import("mobx-state-tree").ISimpleType<"HierarchicalTrackSelectorWidget">;
+    /**
+     * #property
+     */
     collapsed: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
+    /**
+     * #property
+     */
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
 }, {
     selection: ({
@@ -27,28 +42,74 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
     filterText: string;
 } & {
+    /**
+     * #action
+     */
     setSelection(elt: AnyConfigurationModel[]): void;
+    /**
+     * #action
+     */
     addToSelection(elt: AnyConfigurationModel[]): void;
+    /**
+     * #action
+     */
     removeFromSelection(elt: AnyConfigurationModel[]): void;
+    /**
+     * #action
+     */
     clearSelection(): void;
+    /**
+     * #action
+     */
     setView(view: unknown): void;
+    /**
+     * #action
+     */
     toggleCategory(pathName: string): void;
+    /**
+     * #action
+     */
     clearFilterText(): void;
+    /**
+     * #action
+     */
     setFilterText(newText: string): void;
 } & {
-    getRefSeqTrackConf(assemblyName: string): any;
+    /**
+     * #method
+     */
+    getRefSeqTrackConf(assemblyName: string): AnyConfigurationModel | undefined;
 } & {
-    trackConfigurations(assemblyName: string): any[];
+    /**
+     * #getter
+     */
     readonly assemblyNames: string[];
-    connectionTrackConfigurations(assemblyName: string, connection: {
+} & {
+    /**
+     * #method
+     * filter out tracks that don't match the current display types
+     */
+    connectionTrackConfigurations(connection: {
         tracks: AnyConfigurationModel[];
     }): ({
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+    /**
+     * #getter
+     * filter out tracks that don't match the current assembly/display types
+     */
+    readonly trackConfigurations: ({
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
 } & {
-    hierarchy(assemblyName: string): {
+    /**
+     * #getter
+     */
+    readonly hierarchy: {
         name: string;
         id: string;
         children: ({
@@ -64,7 +125,10 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
             children: TreeNode[];
         })[];
     };
-    connectionHierarchy(assemblyName: string, connection: {
+    /**
+     * #method
+     */
+    connectionHierarchy(connection: {
         name: string;
         tracks: AnyConfigurationModel[];
     }): TreeNode[];

package/dist/HierarchicalTrackSelectorWidget/model.js

@@ -24,19 +24,25 @@ function matches(query, conf, session) {
         !!(categories === null || categories === void 0 ? void 0 : categories.filter(c => c.toLowerCase().includes(queryLower)).length));
 }
 exports.matches = matches;
-function filterTracks(tracks, self, assemblyName) {
+function filterTracks(tracks, self) {
     const { assemblyManager } = (0, util_1.getSession)(self);
     const { pluginManager } = (0, util_1.getEnv)(self);
-    const assembly = assemblyManager.get(assemblyName);
-    if (!assembly) {
-        return [];
-    }
-    const { allAliases } = assembly;
+    const { view } = self;
+    const { trackSelectorAnyOverlap } = view;
+    const trackListAssemblies = self.assemblyNames
+        .map(a => assemblyManager.get(a))
+        .filter(util_1.notEmpty);
     return tracks
-        .filter(c => hasAnyOverlap(allAliases, (0, configuration_1.readConfObject)(c, 'assemblyNames')))
         .filter(c => {
-        const { displayTypes } = pluginManager.getViewType(self.view.type);
-        const compatDisplays = displayTypes.map((d) => d.name);
+        const trackAssemblyNames = (0, configuration_1.readConfObject)(c, 'assemblyNames');
+        const trackAssemblies = new Set((trackAssemblyNames === null || trackAssemblyNames === void 0 ? void 0 : trackAssemblyNames.map(name => assemblyManager.get(name)).filter(util_1.notEmpty)) || []);
+        return trackSelectorAnyOverlap
+            ? trackListAssemblies.some(a => trackAssemblies.has(a))
+            : trackListAssemblies.every(a => trackAssemblies.has(a));
+    })
+        .filter(c => {
+        const { displayTypes } = pluginManager.getViewType(view.type);
+        const compatDisplays = displayTypes.map(d => d.name);
         const trackDisplays = c.displays.map((d) => d.type);
         return hasAnyOverlap(compatDisplays, trackDisplays);
     });
@@ -89,12 +95,27 @@ function generateHierarchy(model, trackConfigurations, collapsed, extra) {
     return hierarchy.children;
 }
 exports.generateHierarchy = generateHierarchy;
+/**
+ * #stateModel HierarchicalTrackSelectorWidget
+ */
 function stateTreeFactory(pluginManager) {
     return mobx_state_tree_1.types
         .model('HierarchicalTrackSelectorWidget', {
+        /**
+         * #property
+         */
         id: mst_1.ElementId,
+        /**
+         * #property
+         */
         type: mobx_state_tree_1.types.literal('HierarchicalTrackSelectorWidget'),
+        /**
+         * #property
+         */
         collapsed: mobx_state_tree_1.types.map(mobx_state_tree_1.types.boolean),
+        /**
+         * #property
+         */
         view: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
     })
         .volatile(() => ({
@@ -102,32 +123,59 @@ function stateTreeFactory(pluginManager) {
         filterText: '',
     }))
         .actions(self => ({
+        /**
+         * #action
+         */
         setSelection(elt) {
             self.selection = elt;
         },
+        /**
+         * #action
+         */
         addToSelection(elt) {
             self.selection = (0, util_1.dedupe)([...self.selection, ...elt], e => e.trackId);
         },
+        /**
+         * #action
+         */
         removeFromSelection(elt) {
             self.selection = self.selection.filter(f => !elt.includes(f));
         },
+        /**
+         * #action
+         */
         clearSelection() {
             self.selection = [];
         },
+        /**
+         * #action
+         */
         setView(view) {
             self.view = view;
         },
+        /**
+         * #action
+         */
         toggleCategory(pathName) {
             self.collapsed.set(pathName, !self.collapsed.get(pathName));
         },
+        /**
+         * #action
+         */
         clearFilterText() {
             self.filterText = '';
         },
+        /**
+         * #action
+         */
         setFilterText(newText) {
             self.filterText = newText;
         },
     }))
         .views(self => ({
+        /**
+         * #method
+         */
         getRefSeqTrackConf(assemblyName) {
             const { assemblyManager } = (0, util_1.getSession)(self);
             const assembly = assemblyManager.get(assemblyName);
@@ -141,58 +189,56 @@ function stateTreeFactory(pluginManager) {
                     return trackConf;
                 }
             }
+            return undefined;
         },
     }))
         .views(self => ({
-        trackConfigurations(assemblyName) {
-            if (!self.view) {
-                return [];
-            }
-            const { tracks, assemblyManager } = (0, util_1.getSession)(self);
-            const assembly = assemblyManager.get(assemblyName);
-            if (!assembly) {
-                return [];
-            }
-            const refseq = self.getRefSeqTrackConf(assemblyName);
-            // filter out tracks that don't match the current assembly (check all
-            // assembly aliases) and display types
-            return [
-                ...(refseq ? [refseq] : []),
-                ...filterTracks(tracks, self, assemblyName),
-            ];
-        },
+        /**
+         * #getter
+         */
         get assemblyNames() {
             var _a;
             return ((_a = self.view) === null || _a === void 0 ? void 0 : _a.assemblyNames) || [];
         },
-        connectionTrackConfigurations(assemblyName, connection) {
-            if (!self.view) {
-                return [];
-            }
-            // filter out tracks that don't match the current display types
-            return filterTracks(connection.tracks, self, assemblyName);
+    }))
+        .views(self => ({
+        /**
+         * #method
+         * filter out tracks that don't match the current display types
+         */
+        connectionTrackConfigurations(connection) {
+            return !self.view ? [] : filterTracks(connection.tracks, self);
+        },
+        /**
+         * #getter
+         * filter out tracks that don't match the current assembly/display types
+         */
+        get trackConfigurations() {
+            return !self.view
+                ? []
+                : [
+                    ...self.assemblyNames.map(a => self.getRefSeqTrackConf(a)),
+                    ...filterTracks((0, util_1.getSession)(self).tracks, self),
+                ].filter(util_1.notEmpty);
         },
     }))
         .views(self => ({
-        hierarchy(assemblyName) {
-            const hier = generateHierarchy(
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            self, self.trackConfigurations(assemblyName), self.collapsed);
+        /**
+         * #getter
+         */
+        get hierarchy() {
+            const hier = generateHierarchy(self, self.trackConfigurations, self.collapsed);
             const session = (0, util_1.getSession)(self);
             const { connectionInstances } = session;
-            const { assemblyManager } = (0, util_1.getSession)(self);
-            const assembly = assemblyManager.get(assemblyName);
-            const conns = (assembly &&
-                (connectionInstances === null || connectionInstances === void 0 ? void 0 : connectionInstances.map(c => ({
-                    // @ts-expect-error
-                    id: (0, mobx_state_tree_1.getSnapshot)(c).configuration,
-                    name: (0, configuration_1.getConf)(c, 'name'),
-                    children: this.connectionHierarchy(assemblyName, c),
-                    state: {
-                        expanded: true,
-                    },
-                })).filter(f => f.children.length))) ||
-                [];
+            const conns = (connectionInstances === null || connectionInstances === void 0 ? void 0 : connectionInstances.map(c => ({
+                // @ts-expect-error
+                id: (0, mobx_state_tree_1.getSnapshot)(c).configuration,
+                name: (0, configuration_1.getConf)(c, 'name'),
+                children: this.connectionHierarchy(c),
+                state: {
+                    expanded: true,
+                },
+            })).filter(f => f.children.length)) || [];
             return {
                 name: 'Root',
                 id: 'Root',
@@ -202,10 +248,11 @@ function stateTreeFactory(pluginManager) {
                 ],
             };
         },
-        connectionHierarchy(assemblyName, connection) {
-            return generateHierarchy(
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            self, self.connectionTrackConfigurations(assemblyName, connection), self.collapsed, connection.name);
+        /**
+         * #method
+         */
+        connectionHierarchy(connection) {
+            return generateHierarchy(self, self.connectionTrackConfigurations(connection), self.collapsed, connection.name);
         },
     }));
 }

package/dist/HierarchicalTrackSelectorWidget/model.js.map

@@ -1 +1 @@
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+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/HierarchicalTrackSelectorWidget/model.ts"],"names":[],"mappings":";;;AAAA,qDAA8D;AAC9D,+DAIoC;AACpC,6CAM2B;AAC3B,sDAAwD;AACxD,sDAAwD;AAGxD,SAAS,aAAa,CAAI,KAAU,EAAE,EAAE,KAAU,EAAE;IAClD,iEAAiE;IACjE,iCAAiC;IACjC,IAAI,EAAE,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE;QACnB,OAAO,IAAI,CAAA;KACZ;SAAM;QACL,MAAM,EAAE,GAAG,IAAI,GAAG,CAAC,EAAE,CAAC,CAAA;QACtB,OAAO,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;KAC/B;AACH,CAAC;AAED,SAAgB,OAAO,CACrB,KAAa,EACb,IAA2B,EAC3B,OAA6B;IAE7B,MAAM,UAAU,GAAG,IAAA,8BAAc,EAAC,IAAI,EAAE,UAAU,CAAyB,CAAA;IAC3E,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,EAAE,CAAA;IACtC,OAAO,CACL,IAAA,qBAAY,EAAC,IAAI,EAAE,OAAO,CAAC,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,UAAU,CAAC;QAC9D,CAAC,CAAC,CAAA,UAAU,aAAV,UAAU,uBAAV,UAAU,CAAE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,UAAU,CAAC,EAAE,MAAM,CAAA,CACvE,CAAA;AACH,CAAC;AAXD,0BAWC;AAWD,SAAS,YAAY,CACnB,MAA+B,EAC/B,IAGC;IAED,MAAM,EAAE,eAAe,EAAE,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;IAC5C,MAAM,EAAE,aAAa,EAAE,GAAG,IAAA,aAAM,EAAC,IAAI,CAAC,CAAA;IACtC,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;IACrB,MAAM,EAAE,uBAAuB,EAAE,GAAG,IAAI,CAAA;IACxC,MAAM,mBAAmB,GAAG,IAAI,CAAC,aAAa;SAC3C,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;SAChC,MAAM,CAAC,eAAQ,CAAC,CAAA;IAEnB,OAAO,MAAM;SACV,MAAM,CAAC,CAAC,CAAC,EAAE;QACV,MAAM,kBAAkB,GAAG,IAAA,8BAAc,EAAC,CAAC,EAAE,eAAe,CAAa,CAAA;QACzE,MAAM,eAAe,GAAG,IAAI,GAAG,CAC7B,CAAA,kBAAkB,aAAlB,kBAAkB,uBAAlB,kBAAkB,CACd,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,IAAI,CAAC,EACtC,MAAM,CAAC,eAAQ,CAAC,KAAI,EAAE,CAC1B,CAAA;QACD,OAAO,uBAAuB;YAC5B,CAAC,CAAC,mBAAmB,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;YACvD,CAAC,CAAC,mBAAmB,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;IAC5D,CAAC,CAAC;SACD,MAAM,CAAC,CAAC,CAAC,EAAE;QACV,MAAM,EAAE,YAAY,EAAE,GAAG,aAAa,CAAC,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAC7D,MAAM,cAAc,GAAG,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACpD,MAAM,aAAa,GAAG,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAmB,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACrE,OAAO,aAAa,CAAC,cAAc,EAAE,aAAa,CAAC,CAAA;IACrD,CAAC,CAAC,CAAA;AACN,CAAC;AAED,SAAgB,iBAAiB,CAC/B,KAAqC,EACrC,mBAA4C,EAC5C,SAAwD,EACxD,KAAc;IAEd,MAAM,SAAS,GAAG,EAAE,QAAQ,EAAE,EAAgB,EAAc,CAAA;IAC5D,MAAM,EAAE,UAAU,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;IAClC,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IAEjC,mBAAmB;SAChB,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,OAAO,CAAC,UAAU,EAAE,IAAI,EAAE,OAAO,CAAC,CAAC;SAClD,OAAO,CAAC,IAAI,CAAC,EAAE;QACd,iEAAiE;QACjE,MAAM,UAAU,GAAG,CAAC,GAAG,CAAC,IAAA,8BAAc,EAAC,IAAI,EAAE,UAAU,CAAC,IAAI,EAAE,CAAC,CAAC,CAAA;QAEhE,uEAAuE;QACvE,kEAAkE;QAClE,0BAA0B;QAC1B,IAAI,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,cAAc,CAAC,EAAE;YACzC,UAAU,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;SACtC;QAED,IAAI,SAAS,GAAG,SAAS,CAAA;QAEzB,wDAAwD;QACxD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC1C,MAAM,QAAQ,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YAC9B,MAAM,GAAG,GAAG,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,QAAQ,CAAC,CAAA;YAC7D,MAAM,EAAE,GAAG,KAAK,GAAG,GAAG,GAAG,UAAU,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;YAC7D,IAAI,CAAC,GAAG,EAAE;gBACR,MAAM,CAAC,GAAG;oBACR,QAAQ,EAAE,EAAE;oBACZ,IAAI,EAAE,QAAQ;oBACd,EAAE;oBACF,eAAe,EAAE,CAAC,SAAS,CAAC,GAAG,CAAC,EAAE,CAAC;iBACpC,CAAA;gBACD,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;gBAC1B,SAAS,GAAG,CAAC,CAAA;aACd;iBAAM;gBACL,SAAS,GAAG,GAAG,CAAA;aAChB;SACF;QACD,MAAM,MAAM,GAAG,IAAI,CAAC,MAAoD,CAAA;QAExE,uEAAuE;QACvE,SAAS,CAAC,QAAQ,CAAC,MAAM,CACvB,SAAS,CAAC,QAAQ,CAAC,SAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,QAAQ,CAAC,MAAM,CAAC,EACxD,CAAC,EACD;YACE,EAAE,EAAE,IAAI,CAAC,OAAO;YAChB,IAAI,EAAE,IAAA,qBAAY,EAAC,IAAI,EAAE,OAAO,CAAC;YACjC,IAAI;YACJ,OAAO,EAAE,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,KAAK,IAAI,CAAC;YACnD,QAAQ,EAAE,EAAE;SACb,CACF,CAAA;IACH,CAAC,CAAC,CAAA;IAEJ,OAAO,SAAS,CAAC,QAAQ,CAAA;AAC3B,CAAC;AA5DD,8CA4DC;AAED;;GAEG;AACH,SAAwB,gBAAgB,CAAC,aAA4B;IACnE,OAAO,uBAAK;SACT,KAAK,CAAC,iCAAiC,EAAE;QACxC;;WAEG;QACH,EAAE,EAAE,eAAS;QACb;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,iCAAiC,CAAC;QACtD;;WAEG;QACH,SAAS,EAAE,uBAAK,CAAC,GAAG,CAAC,uBAAK,CAAC,OAAO,CAAC;QACnC;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,aAAa,CACvB,aAAa,CAAC,gBAAgB,CAAC,MAAM,EAAE,YAAY,CAAC,CACrD;KACF,CAAC;SACD,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf,SAAS,EAAE,EAA6B;QACxC,UAAU,EAAE,EAAE;KACf,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,YAAY,CAAC,GAA4B;YACvC,IAAI,CAAC,SAAS,GAAG,GAAG,CAAA;QACtB,CAAC;QACD;;WAEG;QACH,cAAc,CAAC,GAA4B;YACzC,IAAI,CAAC,SAAS,GAAG,IAAA,aAAM,EAAC,CAAC,GAAG,IAAI,CAAC,SAAS,EAAE,GAAG,GAAG,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAA;QACtE,CAAC;QACD;;WAEG;QACH,mBAAmB,CAAC,GAA4B;YAC9C,IAAI,CAAC,SAAS,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAA;QAC/D,CAAC;QACD;;WAEG;QACH,cAAc;YACZ,IAAI,CAAC,SAAS,GAAG,EAAE,CAAA;QACrB,CAAC;QACD;;WAEG;QACH,OAAO,CAAC,IAAa;YACnB,IAAI,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package/dist/PluginStoreWidget/components/CustomPluginForm.d.ts

@@ -1,9 +1,9 @@
-/// <reference types="react" />
+import React from 'react';
 import { PluginStoreModel } from '../model';
 declare function CustomPluginForm({ open, onClose, model, }: {
     open: boolean;
     onClose(): void;
     model: PluginStoreModel;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof CustomPluginForm;
 export default _default;

package/dist/PluginStoreWidget/components/CustomPluginForm.js

@@ -29,6 +29,7 @@ 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 ui_1 = require("@jbrowse/core/ui");
 const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
 // icons
@@ -57,43 +58,19 @@ function CustomPluginForm({ open, onClose, model, }) {
     const [esmPluginUrl, setESMPluginUrl] = (0, react_1.useState)('');
     const [cjsPluginUrl, setCJSPluginUrl] = (0, react_1.useState)('');
     const [advancedOptionsOpen, setAdvancedOptionsOpen] = (0, react_1.useState)(false);
-    function handleChange(event) {
-        const { name, value } = event.target;
-        if (name === 'umdName') {
-            setUMDPluginName(value);
-        }
-        if (name === 'umdUrl') {
-            setUMDPluginUrl(value);
-        }
-        if (name === 'esmUrl') {
-            setESMPluginUrl(value);
-        }
-        if (name === 'cjsUrl') {
-            setCJSPluginUrl(value);
-        }
-    }
-    function handleOpenAdvancedOptions() {
-        setAdvancedOptionsOpen(!advancedOptionsOpen);
-    }
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const { jbrowse } = (0, mobx_state_tree_1.getRoot)(model);
     const ready = Boolean((umdPluginName && umdPluginUrl) || esmPluginUrl || cjsPluginUrl);
     function handleSubmit() {
-        if (!ready) {
-            return;
-        }
-        const pluginDefinition = {};
         if (umdPluginName && umdPluginUrl) {
-            pluginDefinition.name = umdPluginName;
-            pluginDefinition.umdUrl = umdPluginUrl;
+            jbrowse.addPlugin({ name: umdPluginName, umdUrl: umdPluginUrl });
         }
         if (esmPluginUrl) {
-            pluginDefinition.esmUrl = esmPluginUrl;
+            jbrowse.addPlugin({ esmUrl: esmPluginUrl });
         }
         if (cjsPluginUrl) {
-            pluginDefinition.cjsUrl = cjsPluginUrl;
+            jbrowse.addPlugin({ cjsUrl: cjsPluginUrl });
         }
-        jbrowse.addPlugin(pluginDefinition);
     }
     function handleClose() {
         setUMDPluginName('');
@@ -102,13 +79,13 @@ function CustomPluginForm({ open, onClose, model, }) {
         setCJSPluginUrl('');
         onClose();
     }
-    return (react_1.default.createElement(material_1.Dialog, { open: open, onClose: handleClose, title: "Add custom plugin" },
+    return (react_1.default.createElement(ui_1.Dialog, { open: open, onClose: handleClose, title: "Add custom plugin" },
         react_1.default.createElement("form", { onSubmit: handleSubmit },
             react_1.default.createElement(material_1.DialogContent, { className: classes.dialogContent },
                 react_1.default.createElement(material_1.DialogContentText, null, "Enter the name of the plugin and its URL. The name should match what is defined in the plugin's build."),
-                react_1.default.createElement(material_1.TextField, { id: "umd-name-input", name: "umdName", label: "Plugin name", variant: "outlined", value: umdPluginName, onChange: handleChange }),
-                react_1.default.createElement(material_1.TextField, { id: "umd-url-input", name: "umdUrl", label: "Plugin URL", variant: "outlined", value: umdPluginUrl, onChange: handleChange }),
-                react_1.default.createElement(material_1.DialogContentText, { onClick: handleOpenAdvancedOptions },
+                react_1.default.createElement(material_1.TextField, { id: "umd-name-input", name: "umdName", label: "Plugin name", variant: "outlined", value: umdPluginName, onChange: event => setUMDPluginName(event.target.value) }),
+                react_1.default.createElement(material_1.TextField, { id: "umd-url-input", name: "umdUrl", label: "Plugin URL", variant: "outlined", value: umdPluginUrl, onChange: event => setUMDPluginUrl(event.target.value) }),
+                react_1.default.createElement(material_1.DialogContentText, { onClick: () => setAdvancedOptionsOpen(!advancedOptionsOpen) },
                     react_1.default.createElement(IconButton_1.default, { className: cx(classes.expand, {
                             [classes.expandOpen]: advancedOptionsOpen,
                         }), "aria-expanded": advancedOptionsOpen, "aria-label": "show more" },
@@ -117,8 +94,8 @@ function CustomPluginForm({ open, onClose, model, }) {
                 react_1.default.createElement(material_1.Collapse, { in: advancedOptionsOpen },
                     react_1.default.createElement("div", { className: classes.dialogContent },
                         react_1.default.createElement(material_1.DialogContentText, null, "The above fields assume that the plugin is built in UMD format. If your plugin is in another format, or you have additional builds you want to add (such as a CJS build for using NodeJS APIs in desktop), you can enter the URLs for those builds below."),
-                        react_1.default.createElement(material_1.TextField, { id: "esm-url-input", name: "esmUrl", label: "ESM build URL", variant: "outlined", value: esmPluginUrl, onChange: handleChange }),
-                        react_1.default.createElement(material_1.TextField, { id: "cjs-url-input", name: "cjsUrl", label: "CJS build URL", variant: "outlined", value: cjsPluginUrl, onChange: handleChange })))),
+                        react_1.default.createElement(material_1.TextField, { id: "esm-url-input", name: "esmUrl", label: "ESM build URL", variant: "outlined", value: esmPluginUrl, onChange: event => setESMPluginUrl(event.target.value) }),
+                        react_1.default.createElement(material_1.TextField, { id: "cjs-url-input", name: "cjsUrl", label: "CJS build URL", variant: "outlined", value: cjsPluginUrl, onChange: event => setCJSPluginUrl(event.target.value) })))),
             react_1.default.createElement(material_1.DialogActions, null,
                 react_1.default.createElement(material_1.Button, { variant: "contained", onClick: handleClose }, "Cancel"),
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", onClick: handleSubmit, disabled: !ready }, "Submit")))));

package/dist/PluginStoreWidget/components/CustomPluginForm.js.map

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package/dist/PluginStoreWidget/components/InstalledPlugin.d.ts

@@ -1,4 +1,4 @@
-/// <reference types="react" />
+import React from 'react';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { BasePlugin } from '@jbrowse/core/util/types';
 import { PluginStoreModel } from '../model';
@@ -6,6 +6,6 @@ declare function InstalledPlugin({ plugin, model, pluginManager, }: {
     plugin: BasePlugin;
     model: PluginStoreModel;
     pluginManager: PluginManager;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof InstalledPlugin;
 export default _default;

package/dist/PluginStoreWidget/components/InstalledPluginsList.d.ts

@@ -1,9 +1,9 @@
-/// <reference types="react" />
+import React from 'react';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { PluginStoreModel } from '../model';
 declare function InstalledPluginsList({ pluginManager, model, }: {
     pluginManager: PluginManager;
     model: PluginStoreModel;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof InstalledPluginsList;
 export default _default;

package/dist/PluginStoreWidget/components/PluginCard.d.ts

@@ -1,9 +1,9 @@
-/// <reference types="react" />
+import React from 'react';
 import { JBrowsePlugin } from '@jbrowse/core/util/types';
 import { PluginStoreModel } from '../model';
 declare const _default: ({ plugin, model, adminMode, }: {
     plugin: JBrowsePlugin;
     model: PluginStoreModel;
     adminMode: boolean;
-}) => JSX.Element;
+}) => React.JSX.Element;
 export default _default;

package/dist/PluginStoreWidget/components/PluginStoreWidget.d.ts

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

package/dist/PluginStoreWidget/components/PluginStoreWidget.js

@@ -119,14 +119,11 @@ function PluginStoreWidget({ model }) {
                 react_1.default.createElement(material_1.Typography, { variant: "h5" }, "Available plugins")),
             error ? (react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`)) : pluginArray ? (pluginArray
                 .filter(plugin => {
-                // If pugin only has cjsUrl, don't display outside desktop
-                if (!util_1.isElectron &&
-                    !(plugin.esmUrl || plugin.url || plugin.umdUrl)) {
-                    return false;
-                }
-                return plugin.name
-                    .toLowerCase()
-                    .includes(model.filterText.toLowerCase());
+                // If plugin only has cjsUrl, don't display outside desktop
+                return (!(util_1.isElectron && plugin.cjsUrl) &&
+                    plugin.name
+                        .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(ui_1.LoadingEllipses, null)))));
 }