@jbrowse/plugin-data-management 2.17.0 → 2.18.0

package/esm/{ucsc-trackhub → UCSCTrackHub}/model.js

@@ -1,31 +1,16 @@
-import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models';
 import { ConfigurationReference } from '@jbrowse/core/configuration';
+import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models';
 import { types } from 'mobx-state-tree';
-// locals
 import configSchema from './configSchema';
-/**
- * #stateModel UCSCTrackHubConnection
- * extends BaseConnectionModel
- */
 export default function UCSCTrackHubConnection(pluginManager) {
     return types
         .compose('UCSCTrackHubConnection', BaseConnectionModelFactory(pluginManager), types.model({
-        /**
-         * #property
-         */
         configuration: ConfigurationReference(configSchema),
-        /**
-         * #property
-         */
         type: types.literal('UCSCTrackHubConnection'),
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         async connect() {
             const { doConnect } = await import('./doConnect');
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
             doConnect(self);
         },
     }));

package/esm/{ucsc-trackhub → UCSCTrackHub}/ucscAssemblies.js

@@ -1,6 +1,3 @@
-// These are the assemblies for which there is a sequence file located at
-// http://hgdownload.soe.ucsc.edu/goldenPath/${assemblyName}/bigZips/${assemblyName}.2bit
-// This list was generated by `getUcscAssemblies.js`
 export default `ailMel1
 allMis1
 anoCar1

package/esm/{ucsc-trackhub → UCSCTrackHub}/ucscTrackHub.d.ts

@@ -1,5 +1,5 @@
-import { FileLocation } from '@jbrowse/core/util';
 import { GenomesFile, TrackDbFile } from '@gmod/ucsc-hub';
+import type { FileLocation } from '@jbrowse/core/util';
 export declare function fetchGenomesFile(genomesLoc: FileLocation): Promise<GenomesFile>;
 export declare function fetchTrackDbFile(trackDbLoc: FileLocation): Promise<TrackDbFile>;
 export declare function makeLoc(first: string, base: {

package/esm/{ucsc-trackhub → UCSCTrackHub}/ucscTrackHub.js

@@ -1,7 +1,7 @@
-import { isUriLocation, notEmpty, objectHash, } from '@jbrowse/core/util';
+import { GenomesFile, TrackDbFile } from '@gmod/ucsc-hub';
+import { isUriLocation, notEmpty, objectHash } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { generateUnknownTrackConf } from '@jbrowse/core/util/tracks';
-import { GenomesFile, TrackDbFile } from '@gmod/ucsc-hub';
 export async function fetchGenomesFile(genomesLoc) {
     const genomesFileText = await openLocation(genomesLoc).readFile('utf8');
     return new GenomesFile(genomesFileText);
@@ -174,20 +174,6 @@ function makeTrackConfig({ track, categories, trackDbLoc, trackDb, sequenceAdapt
                     hicLocation: bigDataLocation,
                 },
             };
-        // unsupported types
-        //     case 'peptideMapping':
-        //     case 'gvf':
-        //     case 'ld2':
-        //     case 'narrowPeak':
-        //     case 'wig':
-        //     case 'wigMaf':
-        //     case 'halSnake':
-        //     case 'bed':
-        //     case 'bed5FloatScore':
-        //     case 'bedGraph':
-        //     case 'bedRnaElements':
-        //     case 'broadPeak':
-        //     case 'coloredExon':
         default:
             return generateUnknownTrackConf(name, baseTrackType, categories);
     }

package/esm/index.d.ts

@@ -1,20 +1,20 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const AssemblyManager: import("react").LazyExoticComponent<({ rootModel, onClose, }: {
-    rootModel: any;
-    onClose: (arg: boolean) => void;
+import type PluginManager from '@jbrowse/core/PluginManager';
+declare const AssemblyManager: import("react").LazyExoticComponent<({ session, onClose, }: {
+    session: import("@jbrowse/core/util").AbstractSessionModel;
+    onClose: () => void;
 }) => import("react").JSX.Element>;
 export default class DataManagementPlugin extends Plugin {
     name: string;
     exports: {
-        AssemblyManager: import("react").LazyExoticComponent<({ rootModel, onClose, }: {
-            rootModel: any;
-            onClose: (arg: boolean) => void;
+        AssemblyManager: import("react").LazyExoticComponent<({ session, onClose, }: {
+            session: import("@jbrowse/core/util").AbstractSessionModel;
+            onClose: () => void;
         }) => import("react").JSX.Element>;
     };
     install(pluginManager: PluginManager): void;
     configure(_pluginManager: PluginManager): void;
 }
 export { AssemblyManager };
-export { type AddTrackModel } from './AddTrackWidget/model';
-export { type HierarchicalTrackSelectorModel } from './HierarchicalTrackSelectorWidget';
+export type { AddTrackModel } from './AddTrackWidget/model';
+export type { HierarchicalTrackSelectorModel } from './HierarchicalTrackSelectorWidget';

package/esm/index.js

@@ -1,10 +1,10 @@
 import { lazy } from 'react';
 import Plugin from '@jbrowse/core/Plugin';
-import UCSCTrackHubConnectionF from './ucsc-trackhub';
-import AddTrackWidgetF from './AddTrackWidget';
 import AddConnectionWidgetF from './AddConnectionWidget';
-import PluginStoreWidgetF from './PluginStoreWidget';
+import AddTrackWidgetF from './AddTrackWidget';
 import HierarchicalTrackSelectorWidgetF from './HierarchicalTrackSelectorWidget';
+import PluginStoreWidgetF from './PluginStoreWidget';
+import UCSCTrackHubConnectionF from './UCSCTrackHub';
 const AssemblyManager = lazy(() => import('./AssemblyManager'));
 export default class DataManagementPlugin extends Plugin {
     constructor() {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "2.17.0",
+  "version": "2.18.0",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -60,5 +60,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
 }

package/esm/ucsc-trackhub/index.js

@@ -1,13 +0,0 @@
-import { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
-import stateModelFactory from './model';
-import configSchema from './configSchema';
-export default function UCSCTrackHubConnectionF(pluginManager) {
-    pluginManager.addConnectionType(() => new ConnectionType({
-        name: 'UCSCTrackHubConnection',
-        configSchema,
-        stateModel: stateModelFactory(pluginManager),
-        displayName: 'UCSC Track Hub',
-        description: 'A track or assembly hub in the Track Hub format',
-        url: '//genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Intro',
-    }));
-}