@jbrowse/plugin-data-management 2.5.0 → 2.6.2

package/esm/HierarchicalTrackSelectorWidget/model.js

@@ -1,6 +1,6 @@
 import { types, getSnapshot } from 'mobx-state-tree';
 import { getConf, readConfObject, } from '@jbrowse/core/configuration';
-import { dedupe, getSession, getEnv, } from '@jbrowse/core/util';
+import { dedupe, getSession, getEnv, notEmpty, } from '@jbrowse/core/util';
 import { getTrackName } from '@jbrowse/core/util/tracks';
 import { ElementId } from '@jbrowse/core/util/types/mst';
 function hasAnyOverlap(a1 = [], a2 = []) {
@@ -20,19 +20,25 @@ export function matches(query, conf, session) {
     return (getTrackName(conf, session).toLowerCase().includes(queryLower) ||
         !!(categories === null || categories === void 0 ? void 0 : categories.filter(c => c.toLowerCase().includes(queryLower)).length));
 }
-function filterTracks(tracks, self, assemblyName) {
+function filterTracks(tracks, self) {
     const { assemblyManager } = getSession(self);
     const { pluginManager } = 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(notEmpty);
     return tracks
-        .filter(c => hasAnyOverlap(allAliases, readConfObject(c, 'assemblyNames')))
         .filter(c => {
-        const { displayTypes } = pluginManager.getViewType(self.view.type);
-        const compatDisplays = displayTypes.map((d) => d.name);
+        const trackAssemblyNames = readConfObject(c, 'assemblyNames');
+        const trackAssemblies = new Set((trackAssemblyNames === null || trackAssemblyNames === void 0 ? void 0 : trackAssemblyNames.map(name => assemblyManager.get(name)).filter(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);
     });
@@ -84,12 +90,27 @@ export function generateHierarchy(model, trackConfigurations, collapsed, extra)
     });
     return hierarchy.children;
 }
+/**
+ * #stateModel HierarchicalTrackSelectorWidget
+ */
 export default function stateTreeFactory(pluginManager) {
     return types
         .model('HierarchicalTrackSelectorWidget', {
+        /**
+         * #property
+         */
         id: ElementId,
+        /**
+         * #property
+         */
         type: types.literal('HierarchicalTrackSelectorWidget'),
+        /**
+         * #property
+         */
         collapsed: types.map(types.boolean),
+        /**
+         * #property
+         */
         view: types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
     })
         .volatile(() => ({
@@ -97,32 +118,59 @@ export default function stateTreeFactory(pluginManager) {
         filterText: '',
     }))
         .actions(self => ({
+        /**
+         * #action
+         */
         setSelection(elt) {
             self.selection = elt;
         },
+        /**
+         * #action
+         */
         addToSelection(elt) {
             self.selection = 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 } = getSession(self);
             const assembly = assemblyManager.get(assemblyName);
@@ -136,58 +184,56 @@ export default function stateTreeFactory(pluginManager) {
                     return trackConf;
                 }
             }
+            return undefined;
         },
     }))
         .views(self => ({
-        trackConfigurations(assemblyName) {
-            if (!self.view) {
-                return [];
-            }
-            const { tracks, assemblyManager } = 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(getSession(self).tracks, self),
+                ].filter(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 = getSession(self);
             const { connectionInstances } = session;
-            const { assemblyManager } = getSession(self);
-            const assembly = assemblyManager.get(assemblyName);
-            const conns = (assembly &&
-                (connectionInstances === null || connectionInstances === void 0 ? void 0 : connectionInstances.map(c => ({
-                    // @ts-expect-error
-                    id: getSnapshot(c).configuration,
-                    name: 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: getSnapshot(c).configuration,
+                name: getConf(c, 'name'),
+                children: this.connectionHierarchy(c),
+                state: {
+                    expanded: true,
+                },
+            })).filter(f => f.children.length)) || [];
             return {
                 name: 'Root',
                 id: 'Root',
@@ -197,11 +243,11 @@ export default 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);
         },
     }));
 }
-//# sourceMappingURL=model.js.map

package/esm/PluginStoreWidget/components/CustomPluginForm.d.ts

@@ -1,8 +1,9 @@
+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/esm/PluginStoreWidget/components/CustomPluginForm.js

@@ -73,4 +73,3 @@ function CustomPluginForm({ open, onClose, model, }) {
                 React.createElement(Button, { variant: "contained", color: "primary", onClick: handleSubmit, disabled: !ready }, "Submit")))));
 }
 export default observer(CustomPluginForm);
-//# sourceMappingURL=CustomPluginForm.js.map

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

@@ -1,3 +1,4 @@
+import React from 'react';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { BasePlugin } from '@jbrowse/core/util/types';
 import { PluginStoreModel } from '../model';
@@ -5,6 +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/esm/PluginStoreWidget/components/InstalledPlugin.js

@@ -74,4 +74,3 @@ function InstalledPlugin({ plugin, model, pluginManager, }) {
             React.createElement(Typography, null, plugin.name))));
 }
 export default observer(InstalledPlugin);
-//# sourceMappingURL=InstalledPlugin.js.map

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

@@ -1,8 +1,9 @@
+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/esm/PluginStoreWidget/components/InstalledPluginsList.js

@@ -13,4 +13,3 @@ function InstalledPluginsList({ pluginManager, model, }) {
         .map(plugin => (React.createElement(InstalledPlugin, { key: plugin.name, plugin: plugin, model: model, pluginManager: pluginManager })))) : (React.createElement(Typography, null, "No plugins currently installed"))));
 }
 export default observer(InstalledPluginsList);
-//# sourceMappingURL=InstalledPluginsList.js.map

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

@@ -1,8 +1,9 @@
+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/esm/PluginStoreWidget/components/PluginCard.js

@@ -58,4 +58,3 @@ export default observer(function PluginCard({ plugin, model, adminMode, }) {
                     setTempDisabled(true);
                 } }, isInstalled ? 'Installed' : 'Install'))));
 });
-//# sourceMappingURL=PluginCard.js.map

package/esm/PluginStoreWidget/components/PluginStoreWidget.d.ts

@@ -1,6 +1,7 @@
+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/esm/PluginStoreWidget/components/PluginStoreWidget.js

@@ -100,4 +100,3 @@ function PluginStoreWidget({ model }) {
                 .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/index.js

@@ -14,4 +14,3 @@ export default (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/esm/PluginStoreWidget/model.js

@@ -17,4 +17,3 @@ export default function f(pluginManager) {
         },
     }));
 }
-//# sourceMappingURL=model.js.map

package/esm/SetDefaultSession/SetDefaultSession.d.ts

@@ -1,5 +1,6 @@
+import React from 'react';
 declare const SetDefaultSession: ({ rootModel, onClose }: {
     rootModel?: unknown;
     onClose: () => void;
-}) => JSX.Element | null;
+}) => React.JSX.Element | null;
 export default SetDefaultSession;

package/esm/SetDefaultSession/SetDefaultSession.js

@@ -31,4 +31,3 @@ const SetDefaultSession = observer(({ rootModel, onClose }) => {
                 } }, "Set current session as default"))));
 });
 export default SetDefaultSession;
-//# sourceMappingURL=SetDefaultSession.js.map

package/esm/SetDefaultSession/index.js

@@ -1,2 +1 @@
 export { default } from './SetDefaultSession';
-//# sourceMappingURL=index.js.map

package/esm/index.d.ts

@@ -4,22 +4,22 @@ import PluginManager from '@jbrowse/core/PluginManager';
 declare const SetDefaultSession: import("react").LazyExoticComponent<({ rootModel, onClose }: {
     rootModel?: unknown;
     onClose: () => void;
-}) => JSX.Element | null>;
+}) => import("react").JSX.Element | null>;
 declare const AssemblyManager: import("react").LazyExoticComponent<({ rootModel, onClose, }: {
     rootModel: any;
     onClose: (arg: boolean) => void;
-}) => JSX.Element>;
+}) => import("react").JSX.Element>;
 export default class extends Plugin {
     name: string;
     exports: {
         AssemblyManager: import("react").LazyExoticComponent<({ rootModel, onClose, }: {
             rootModel: any;
             onClose: (arg: boolean) => void;
-        }) => JSX.Element>;
+        }) => import("react").JSX.Element>;
         SetDefaultSession: import("react").LazyExoticComponent<({ rootModel, onClose }: {
             rootModel?: unknown;
             onClose: () => void;
-        }) => JSX.Element | null>;
+        }) => import("react").JSX.Element | null>;
     };
     install(pluginManager: PluginManager): void;
     configure(_pluginManager: PluginManager): void;

package/esm/index.js

@@ -26,4 +26,3 @@ export default class extends Plugin {
     configure(_pluginManager) { }
 }
 export { AssemblyManager, SetDefaultSession };
-//# sourceMappingURL=index.js.map

package/esm/ucsc-trackhub/configSchema.js

@@ -31,4 +31,3 @@ const UCSCTrackHubConnection = ConfigurationSchema('UCSCTrackHubConnection', {
     baseConfiguration: baseConnectionConfig,
 });
 export default UCSCTrackHubConnection;
-//# sourceMappingURL=configSchema.js.map

package/esm/ucsc-trackhub/index.js

@@ -11,4 +11,3 @@ export default (pluginManager) => {
         url: '//genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Intro',
     }));
 };
-//# sourceMappingURL=index.js.map

package/esm/ucsc-trackhub/model.d.ts

@@ -2,6 +2,18 @@ import PluginManager from '@jbrowse/core/PluginManager';
 export default function UCSCTrackHubConnection(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     name: import("mobx-state-tree").ISimpleType<string>;
     tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        name: {
+            type: string;
+            defaultValue: string;
+            description: string;
+        };
+        assemblyNames: {
+            type: string;
+            defaultValue: never[];
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
 } & {
     configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         hubTxtLocation: {

package/esm/ucsc-trackhub/model.js

@@ -4,7 +4,6 @@ import { getSession } from '@jbrowse/core/util';
 import { types } from 'mobx-state-tree';
 // locals
 import configSchema from './configSchema';
-import { fetchGenomesFile, fetchHubFile, fetchTrackDbFile, generateTracks, } from './ucscTrackHub';
 export default function UCSCTrackHubConnection(pluginManager) {
     return types
         .compose('UCSCTrackHubConnection', BaseConnectionModelFactory(pluginManager), types.model({
@@ -15,9 +14,10 @@ export default function UCSCTrackHubConnection(pluginManager) {
         async connect() {
             var _a;
             const session = getSession(self);
+            const notLoadedAssemblies = [];
             try {
-                const connectionName = getConf(self, 'name'); // NOTE: name comes from the base configuration
                 const hubFileLocation = getConf(self, 'hubTxtLocation');
+                const { generateTracks, fetchGenomesFile, fetchTrackDbFile, fetchHubFile, } = await import('./ucscTrackHub');
                 const hubFile = await fetchHubFile(hubFileLocation);
                 const genomeFile = hubFile.get('genomesFile');
                 if (!genomeFile) {
@@ -34,7 +34,7 @@ export default function UCSCTrackHubConnection(pluginManager) {
                         locationType: 'LocalPathLocation',
                     };
                 const genomesFile = await fetchGenomesFile(genomesFileLocation);
-                const trackDbData = [];
+                const map = {};
                 for (const [genomeName, genome] of genomesFile) {
                     const assemblyNames = getConf(self, 'assemblyNames');
                     if (assemblyNames.length > 0 &&
@@ -43,14 +43,15 @@ export default function UCSCTrackHubConnection(pluginManager) {
                     }
                     const conf = (_a = session.assemblyManager.get(genomeName)) === null || _a === void 0 ? void 0 : _a.configuration;
                     if (!conf) {
-                        throw new Error(`Cannot find assembly for "${genomeName}" from the genomes file for connection "${connectionName}"`);
+                        notLoadedAssemblies.push(genomeName);
+                        continue;
                     }
                     const db = genome.get('trackDb');
                     if (!db) {
                         throw new Error('genomesFile not found on hub');
                     }
                     const base = new URL(genomeFile, hubUri);
-                    const trackDbLoc = hubUri
+                    const loc = hubUri
                         ? {
                             uri: new URL(db, base).href,
                             locationType: 'UriLocation',
@@ -59,13 +60,22 @@ export default function UCSCTrackHubConnection(pluginManager) {
                             localPath: db,
                             locationType: 'LocalPathLocation',
                         };
-                    const trackDb = await fetchTrackDbFile(trackDbLoc);
-                    trackDbData.push([trackDbLoc, trackDb, genomeName, conf]);
-                }
-                for (const [trackDbLoc, trackDbFile, genomeName, conf,] of trackDbData) {
+                    const trackDb = await fetchTrackDbFile(loc);
                     const seqAdapter = readConfObject(conf, ['sequence', 'adapter']);
-                    self.addTrackConfs(generateTracks(trackDbFile, trackDbLoc, genomeName, seqAdapter));
+                    const tracks = generateTracks(trackDb, loc, genomeName, seqAdapter);
+                    self.addTrackConfs(tracks);
+                    map[genomeName] = tracks.length;
                 }
+                const loadedAssemblies = Object.entries(map);
+                const str1 = loadedAssemblies.length
+                    ? `Loaded data from these assemblies: ${loadedAssemblies
+                        .map(([key, val]) => `${key} (${val} tracks)`)
+                        .join(', ')}`
+                    : '';
+                const str2 = notLoadedAssemblies.length
+                    ? `Skipped data from these assemblies: ${notLoadedAssemblies.join(', ')}`
+                    : '';
+                session.notify([str1, str2].filter(f => !!f).join('. '), 'success');
             }
             catch (e) {
                 console.error(e);
@@ -75,4 +85,3 @@ export default function UCSCTrackHubConnection(pluginManager) {
         },
     }));
 }
-//# sourceMappingURL=model.js.map

package/esm/ucsc-trackhub/ucscAssemblies.js

@@ -198,4 +198,3 @@ xenTro2
 xenTro3
 xenTro7
 xenTro9`.split(/\r?\n/);
-//# sourceMappingURL=ucscAssemblies.js.map

package/esm/ucsc-trackhub/ucscTrackHub.js

@@ -288,4 +288,3 @@ function makeTrackConfig(track, categories, trackDbLoc, trackDb, sequenceAdapter
     }
 }
 export { default as ucscAssemblies } from './ucscAssemblies';
-//# sourceMappingURL=ucscTrackHub.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "2.5.0",
+  "version": "2.6.2",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -20,7 +20,6 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src",
     "esm"
   ],
   "scripts": {
@@ -33,7 +32,7 @@
     "useSrc": "node ../../scripts/useSrc.js",
     "prebuild": "npm run clean",
     "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
@@ -61,5 +60,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
+  "gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
 }

package/dist/AddConnectionWidget/components/AddConnectionWidget.js.map

@@ -1 +0,0 @@
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package/dist/AddConnectionWidget/components/ConfigureConnection.js.map

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package/dist/AddConnectionWidget/components/ConnectionTypeSelect.js.map

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package/dist/AddConnectionWidget/index.js.map

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package/dist/AddConnectionWidget/model.js.map

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

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package/dist/AddTrackWidget/components/ConfirmTrack.js.map

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package/dist/AddTrackWidget/components/DefaultAddTrackWorkflow.js.map

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

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package/dist/AddTrackWidget/components/TextIndexingConfig.js.map

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