@jbrowse/plugin-legacy-jbrowse 5.0.0-beta.1 → 5.0.0-beta.10

package/esm/JBrowse1Connection/configSchema.d.ts

@@ -17,35 +17,51 @@
  * ```
  */
 declare const JBrowse1Connection: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
-    readonly dataDirLocation: {
-        readonly type: "fileLocation";
-        readonly defaultValue: {
-            readonly uri: "https://mysite.com/jbrowse/data/";
-            readonly locationType: "UriLocation";
-        };
-        readonly description: "the location of the JBrowse 1 data directory, often something like https://mysite.com/jbrowse/data/";
-    };
-    /**
-     * #slot
-     */
-    readonly assemblyNames: {
-        readonly description: "name of the assembly the connection belongs to, should be a single entry";
-        readonly type: "stringArray";
-        readonly defaultValue: readonly [];
+    assemblyNames: {
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
+    };
+    connectionId: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
+    dataDirLocation: {
+        type: "fileLocation";
+    } & {
+        defaultValue: unknown;
+    };
+    name: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
     };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     readonly name: {
-        readonly type: "string";
-        readonly defaultValue: "nameOfConnection";
-        readonly description: "a unique name for this connection";
+        type: "string";
+    } & {
+        defaultValue: string;
     };
     readonly assemblyNames: {
-        readonly type: "stringArray";
-        readonly defaultValue: readonly [];
-        readonly description: "optional list of names of assemblies in this connection";
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
+    };
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
+    connectionId: {
+        type: "string";
+    } & {
+        defaultValue: string;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId", true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
 export default JBrowse1Connection;

package/esm/JBrowse1Connection/jb1ToJb2.d.ts

@@ -9,7 +9,7 @@ interface Jb2Track {
     displays?: {
         type: string;
         displayId: string;
-        defaultRendering: string;
+        mark: string;
     }[];
 }
 interface Jb2Adapter {

package/esm/JBrowse1Connection/jb1ToJb2.js

@@ -42,21 +42,21 @@ const NO_ADAPTER = {
     'Sequence/StaticChunked': 'StaticChunked',
 };
 /**
- * `defaultRendering` is a slot on LinearWiggleDisplay, not on the track — a
- * track-level one is a key JBrowse does not declare, and is ignored.
+ * `mark` is a slot on LinearWiggleDisplay, not on the track — a track-level
+ * one is a key JBrowse does not declare, and is ignored.
  */
 function wiggleDisplays(jb1TrackConfig, jb2TrackConfig) {
-    const rendering = jb1TrackConfig.type?.endsWith('Density')
-        ? 'density'
+    const mark = jb1TrackConfig.type?.endsWith('Density')
+        ? 'heatmap'
         : jb1TrackConfig.type?.endsWith('XYPlot')
-            ? 'xyplot'
+            ? 'bar'
             : undefined;
-    return rendering
+    return mark
         ? [
             {
                 type: 'LinearWiggleDisplay',
                 displayId: `${jb2TrackConfig.trackId}-LinearWiggleDisplay`,
-                defaultRendering: rendering,
+                mark,
             },
         ]
         : undefined;

package/esm/JBrowse1Connection/model.d.ts

@@ -5,47 +5,79 @@ import type PluginManager from '@jbrowse/core/PluginManager';
  * composed on the base connection model.
  */
 export default function stateModelFactory(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<Omit<{
-    tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
+    tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
     configuration: import("@jbrowse/core/configuration/configurationSchema").IConfigurationReference<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly name: {
-            readonly type: "string";
-            readonly defaultValue: "nameOfConnection";
-            readonly description: "a unique name for this connection";
+            type: "string";
+        } & {
+            defaultValue: string;
         };
         readonly assemblyNames: {
-            readonly type: "stringArray";
-            readonly defaultValue: readonly [];
-            readonly description: "optional list of names of assemblies in this connection";
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>;
+        type: {
+            type: "string";
+        } & {
+            defaultValue: string;
+        };
+        connectionId: {
+            type: "string";
+        } & {
+            defaultValue: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId", true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>;
     silent: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }, "configuration" | "type"> & {
     configuration: import("@jbrowse/core/configuration/configurationSchema").IConfigurationReference<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        readonly dataDirLocation: {
-            readonly type: "fileLocation";
-            readonly defaultValue: {
-                readonly uri: "https://mysite.com/jbrowse/data/";
-                readonly locationType: "UriLocation";
-            };
-            readonly description: "the location of the JBrowse 1 data directory, often something like https://mysite.com/jbrowse/data/";
+        assemblyNames: {
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
         };
-        readonly assemblyNames: {
-            readonly description: "name of the assembly the connection belongs to, should be a single entry";
-            readonly type: "stringArray";
-            readonly defaultValue: readonly [];
+        connectionId: {
+            type: "string";
+        } & {
+            defaultValue: string;
+        };
+        dataDirLocation: {
+            type: "fileLocation";
+        } & {
+            defaultValue: unknown;
+        };
+        name: {
+            type: "string";
+        } & {
+            defaultValue: string;
+        };
+        type: {
+            type: "string";
+        } & {
+            defaultValue: string;
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly name: {
-            readonly type: "string";
-            readonly defaultValue: "nameOfConnection";
-            readonly description: "a unique name for this connection";
+            type: "string";
+        } & {
+            defaultValue: string;
         };
         readonly assemblyNames: {
-            readonly type: "stringArray";
-            readonly defaultValue: readonly [];
-            readonly description: "optional list of names of assemblies in this connection";
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
+        };
+        type: {
+            type: "string";
+        } & {
+            defaultValue: string;
+        };
+        connectionId: {
+            type: "string";
+        } & {
+            defaultValue: string;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId", true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>;
     type: import("@jbrowse/mobx-state-tree").ILiteralType<"JBrowse1Connection">;
 }, {
     loading: boolean;
@@ -57,18 +89,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     setLoading(loading: boolean): void;
 } & {
     afterAttach(): void;
-    addTrackConf(trackConf: Record<string, unknown> | (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
-        setSubschema(slotName: string, data: Record<string, unknown>): any;
-        setSlot(slotName: string, value: unknown): void;
-    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
-    addTrackConfs(trackConfs: (Record<string, unknown> | (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
-        setSubschema(slotName: string, data: Record<string, unknown>): any;
-        setSlot(slotName: string, value: unknown): void;
-    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
-    setTrackConfs(trackConfs: (Record<string, unknown> | (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
-        setSubschema(slotName: string, data: Record<string, unknown>): any;
-        setSlot(slotName: string, value: unknown): void;
-    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
+    addTrackConf(trackConf: Record<string, unknown> | import("@jbrowse/core/configuration").AnyConfigurationModel): (import("@jbrowse/core/configuration").PluggableConfigNode & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>) | undefined;
+    addTrackConfs(trackConfs: (Record<string, unknown> | import("@jbrowse/core/configuration").AnyConfigurationModel)[]): void;
+    setTrackConfs(trackConfs: (Record<string, unknown> | import("@jbrowse/core/configuration").AnyConfigurationModel)[]): void;
 } & {
     connect(): Promise<void>;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;

package/esm/JBrowse1TextSearchAdapter/HttpMap.d.ts

@@ -34,8 +34,9 @@ export default class HttpMap {
      * Loads a file using the url and provided id.
      * Returns response object with contents of the file
      * @param id - string
+     * @param ifMissing - the contents a 404 stands for, if it is not an error
      */
-    loadFile(id: string): Promise<any>;
+    loadFile(id: string, ifMissing?: object): Promise<any>;
     /**
      * Returns the corresponding path of the file given a hex string
      * @param hex - hex string

package/esm/JBrowse1TextSearchAdapter/HttpMap.js

@@ -27,13 +27,16 @@ export default class HttpMap {
      * loads meta.json file from names directory and reads number of hash_bits used
      */
     async readMeta() {
-        if (!this.metaPromise) {
-            this.metaPromise = this.loadFile('meta.json').then(meta => ({
-                hashHexCharacters: Math.ceil(meta.hash_bits / 4),
-                compress: meta.compress,
-                tracks: meta.track_names,
-            }));
-        }
+        this.metaPromise ??= this.loadFile('meta.json')
+            .then(meta => ({
+            hashHexCharacters: Math.ceil(meta.hash_bits / 4),
+            compress: meta.compress,
+            tracks: meta.track_names,
+        }))
+            .catch((e) => {
+            this.metaPromise = undefined;
+            throw e;
+        });
         return this.metaPromise;
     }
     async getHashHexCharacters() {
@@ -60,16 +63,22 @@ export default class HttpMap {
     async getBucket(key) {
         const bucketIdent = this.hash(key);
         const hexToDirPath = await this.hexToDirPath(bucketIdent);
-        return this.loadFile(hexToDirPath);
+        // generate-names.pl writes only the buckets that hold a name, so a missing
+        // one is an empty bucket, as JBrowse 1's own Store/Hash reads it
+        return this.loadFile(hexToDirPath, {});
     }
     /**
      * Loads a file using the url and provided id.
      * Returns response object with contents of the file
      * @param id - string
+     * @param ifMissing - the contents a 404 stands for, if it is not an error
      */
-    async loadFile(id) {
+    async loadFile(id, ifMissing) {
         const response = await fetch(`${this.url}${id}`);
-        if (!response.ok) {
+        if (response.status === 404 && ifMissing) {
+            return ifMissing;
+        }
+        else if (!response.ok) {
             throw new Error(`HTTP ${response.status} ${response.statusText}`);
         }
         return response.json();

package/esm/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.d.ts

@@ -14,7 +14,6 @@ interface SearchResults {
 type IndexFile = Record<string, SearchResults>;
 export default class JBrowse1TextSearchAdapter extends BaseAdapter implements BaseTextSearchAdapter {
     httpMap: HttpMap;
-    tracksNames?: string[];
     constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
     /**
      * Returns the contents of the file containing the query if it exists

package/esm/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.js

@@ -5,7 +5,6 @@ import HttpMap from './HttpMap.js';
 // Uses index built by generate-names.pl
 export default class JBrowse1TextSearchAdapter extends BaseAdapter {
     httpMap;
-    tracksNames;
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
         const namesIndex = readConfObject(config, 'namesIndexLocation');
@@ -24,7 +23,7 @@ export default class JBrowse1TextSearchAdapter extends BaseAdapter {
     }
     async searchIndex(args) {
         const { searchType, queryString } = args;
-        const tracks = this.tracksNames ?? (await this.httpMap.getTrackNames());
+        const tracks = await this.httpMap.getTrackNames();
         const str = queryString.toLowerCase();
         const entries = await this.loadIndexFile(str);
         const results = entries[str];

package/esm/JBrowse1TextSearchAdapter/configSchema.d.ts

@@ -11,39 +11,31 @@
  * ```js
  * {
  *   type: 'JBrowse1TextSearchAdapter',
- *   textSearchAdapterId: 'jbrowse1-names',
  *   namesIndexLocation: { uri: 'https://example.com/jbrowse1/data/names/' },
  *   assemblyNames: ['hg19'],
  * }
  * ```
  */
 declare const _default: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
     readonly namesIndexLocation: {
-        readonly type: "fileLocation";
-        readonly defaultValue: {
-            readonly uri: "/volvox/names";
-            readonly locationType: "UriLocation";
-        };
-        readonly description: "the location of the JBrowse1 names index data directory";
+        type: "fileLocation";
+    } & {
+        defaultValue: unknown;
     };
-    /**
-     * #slot
-     */
     readonly tracks: {
-        readonly type: "stringArray";
-        readonly defaultValue: readonly [];
-        readonly description: "List of tracks covered by text search adapter";
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
     };
-    /**
-     * #slot
-     */
     readonly assemblyNames: {
-        readonly type: "stringArray";
-        readonly defaultValue: readonly [];
-        readonly description: "List of assemblies covered by text search adapter";
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "textSearchAdapterId">>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
 export default _default;

package/esm/JBrowse1TextSearchAdapter/configSchema.js

@@ -12,7 +12,6 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration';
  * ```js
  * {
  *   type: 'JBrowse1TextSearchAdapter',
- *   textSearchAdapterId: 'jbrowse1-names',
  *   namesIndexLocation: { uri: 'https://example.com/jbrowse1/data/names/' },
  *   assemblyNames: ['hg19'],
  * }
@@ -43,10 +42,4 @@ export default ConfigurationSchema('JBrowse1TextSearchAdapter', {
         defaultValue: [],
         description: 'List of assemblies covered by text search adapter',
     },
-}, {
-    explicitlyTyped: true,
-    /**
-     * #identifier
-     */
-    explicitIdentifier: 'textSearchAdapterId',
-});
+}, { explicitlyTyped: true });

package/esm/NCListAdapter/NCListAdapter.d.ts

@@ -14,7 +14,7 @@ export default class NCListAdapter extends BaseFeatureDataAdapter {
     /**
      * Fetch features for a certain region.
      * @param region -
-     * @param opts - [stopToken] optional stopTokenling object for aborting the fetch
+     * @param opts - [signal] optional signalling object for aborting the fetch
      * @returns Observable of Feature objects in the region
      */
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;

package/esm/NCListAdapter/NCListAdapter.js

@@ -1,7 +1,7 @@
 import NCListStore from '@gmod/nclist';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { checkAbortSignal } from '@jbrowse/core/util/aborting';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { checkStopToken } from '@jbrowse/core/util/stopToken';
 import { RemoteFile } from 'generic-filehandle2';
 import NCListFeature from './NCListFeature.js';
 export default class NCListAdapter extends BaseFeatureDataAdapter {
@@ -23,18 +23,18 @@ export default class NCListAdapter extends BaseFeatureDataAdapter {
     /**
      * Fetch features for a certain region.
      * @param region -
-     * @param opts - [stopToken] optional stopTokenling object for aborting the fetch
+     * @param opts - [signal] optional signalling object for aborting the fetch
      * @returns Observable of Feature objects in the region
      */
     getFeatures(region, opts = {}) {
         return ObservableCreate(async (observer) => {
-            const { stopToken } = opts;
+            const { signal } = opts;
             for await (const feature of this.nclist.getFeatures(region)) {
-                checkStopToken(stopToken);
+                checkAbortSignal(signal);
                 observer.next(this.wrapFeature(feature));
             }
             observer.complete();
-        });
+        }, opts.signal);
     }
     wrapFeature(ncFeature) {
         return new NCListFeature(ncFeature, undefined, `${this.id}-${ncFeature.id()}`);

package/esm/NCListAdapter/configSchema.d.ts

@@ -16,26 +16,20 @@
  * ```
  */
 declare const NCListAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     * URL of a JBrowse 1 NCList `trackData.json`, with `{refseq}` standing in
-     * for the reference sequence name — the per-reference directory layout
-     * `flatfile-to-json.pl` and `biodb-to-json.pl` write.
-     */
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
     readonly rootUrlTemplate: {
-        readonly type: "fileLocation";
-        readonly defaultValue: {
-            readonly uri: "/path/to/my/{refseq}/trackData.json";
-            readonly locationType: "UriLocation";
-        };
+        type: "fileLocation";
+    } & {
+        defaultValue: unknown;
     };
-    /**
-     * #slot
-     */
     readonly refNames: {
-        readonly type: "stringArray";
-        readonly defaultValue: readonly [];
-        readonly description: "List of refNames used by the NCList used for aliasing";
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
 export default NCListAdapter;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "5.0.0-beta.1",
+  "version": "5.0.0-beta.10",
   "type": "module",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
@@ -22,12 +22,12 @@
   ],
   "dependencies": {
     "@gmod/nclist": "^3.0.14",
-    "@jbrowse/mobx-state-tree": "^6.5.1",
+    "@jbrowse/mobx-state-tree": "^6.6.1",
     "generic-filehandle2": "^2.4.0",
-    "mobx": "^7.0.3",
+    "mobx": "^7.0.5",
     "rxjs": "^7.8.2",
-    "@jbrowse/add-track-core": "^5.0.0-beta.1",
-    "@jbrowse/core": "^5.0.0-beta.1"
+    "@jbrowse/add-track-core": "^5.0.0-beta.10",
+    "@jbrowse/core": "^5.0.0-beta.10"
   },
   "publishConfig": {
     "access": "public"