@jbrowse/core 3.5.0 → 3.5.1

package/assemblyManager/assemblyManager.d.ts

@@ -14,18 +14,18 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         refNameAliases: {
             [x: string]: string;
         } | undefined;
-        lowerCaseRefNameAliases: {
-            [x: string]: string;
-        } | undefined;
         cytobands: import("../util").Feature[] | undefined;
     } & {
         getConf(arg: string): any;
+        readonly lowerCaseRefNameAliases: {
+            [k: string]: string;
+        } | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
         readonly regions: import("./assembly").BasicRegion[] | undefined;
         readonly aliases: string[];
-        readonly displayName: string | undefined;
+        readonly displayName: string;
         hasName(name: string): boolean;
         readonly allAliases: string[];
         readonly allRefNames: string[] | undefined;
@@ -40,22 +40,17 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
+        setLoaded({ regions, refNameAliases, cytobands, }: {
             regions: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
-            lowerCaseRefNameAliases: {
-                [x: string]: string;
-            };
             cytobands: import("../util").Feature[];
         }): void;
         setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCaseAliases: {
-            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         setLoadingP(p?: Promise<void>): void;
@@ -75,6 +70,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string;
         }>;
+        afterCreate(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
 }, {
     readonly assemblyNameMap: Record<string, {
@@ -86,18 +82,18 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         refNameAliases: {
             [x: string]: string;
         } | undefined;
-        lowerCaseRefNameAliases: {
-            [x: string]: string;
-        } | undefined;
         cytobands: import("../util").Feature[] | undefined;
     } & {
         getConf(arg: string): any;
+        readonly lowerCaseRefNameAliases: {
+            [k: string]: string;
+        } | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
         readonly regions: import("./assembly").BasicRegion[] | undefined;
         readonly aliases: string[];
-        readonly displayName: string | undefined;
+        readonly displayName: string;
         hasName(name: string): boolean;
         readonly allAliases: string[];
         readonly allRefNames: string[] | undefined;
@@ -112,22 +108,17 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
+        setLoaded({ regions, refNameAliases, cytobands, }: {
             regions: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
-            lowerCaseRefNameAliases: {
-                [x: string]: string;
-            };
             cytobands: import("../util").Feature[];
         }): void;
         setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCaseAliases: {
-            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         setLoadingP(p?: Promise<void>): void;
@@ -147,6 +138,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string;
         }>;
+        afterCreate(): void;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
     }, {
@@ -156,18 +148,18 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         refNameAliases: {
             [x: string]: string;
         } | undefined;
-        lowerCaseRefNameAliases: {
-            [x: string]: string;
-        } | undefined;
         cytobands: import("../util").Feature[] | undefined;
     } & {
         getConf(arg: string): any;
+        readonly lowerCaseRefNameAliases: {
+            [k: string]: string;
+        } | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
         readonly regions: import("./assembly").BasicRegion[] | undefined;
         readonly aliases: string[];
-        readonly displayName: string | undefined;
+        readonly displayName: string;
         hasName(name: string): boolean;
         readonly allAliases: string[];
         readonly allRefNames: string[] | undefined;
@@ -182,22 +174,17 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
+        setLoaded({ regions, refNameAliases, cytobands, }: {
             regions: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
-            lowerCaseRefNameAliases: {
-                [x: string]: string;
-            };
             cytobands: import("../util").Feature[];
         }): void;
         setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCaseAliases: {
-            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         setLoadingP(p?: Promise<void>): void;
@@ -217,6 +204,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string;
         }>;
+        afterCreate(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
 } & {
     get(asmName: string): ({
@@ -228,18 +216,18 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         refNameAliases: {
             [x: string]: string;
         } | undefined;
-        lowerCaseRefNameAliases: {
-            [x: string]: string;
-        } | undefined;
         cytobands: import("../util").Feature[] | undefined;
     } & {
         getConf(arg: string): any;
+        readonly lowerCaseRefNameAliases: {
+            [k: string]: string;
+        } | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
         readonly regions: import("./assembly").BasicRegion[] | undefined;
         readonly aliases: string[];
-        readonly displayName: string | undefined;
+        readonly displayName: string;
         hasName(name: string): boolean;
         readonly allAliases: string[];
         readonly allRefNames: string[] | undefined;
@@ -254,22 +242,17 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
+        setLoaded({ regions, refNameAliases, cytobands, }: {
             regions: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
-            lowerCaseRefNameAliases: {
-                [x: string]: string;
-            };
             cytobands: import("../util").Feature[];
         }): void;
         setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCaseAliases: {
-            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         setLoadingP(p?: Promise<void>): void;
@@ -289,6 +272,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string;
         }>;
+        afterCreate(): void;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
     }, {
@@ -298,18 +282,18 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         refNameAliases: {
             [x: string]: string;
         } | undefined;
-        lowerCaseRefNameAliases: {
-            [x: string]: string;
-        } | undefined;
         cytobands: import("../util").Feature[] | undefined;
     } & {
         getConf(arg: string): any;
+        readonly lowerCaseRefNameAliases: {
+            [k: string]: string;
+        } | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
         readonly regions: import("./assembly").BasicRegion[] | undefined;
         readonly aliases: string[];
-        readonly displayName: string | undefined;
+        readonly displayName: string;
         hasName(name: string): boolean;
         readonly allAliases: string[];
         readonly allRefNames: string[] | undefined;
@@ -324,22 +308,17 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
+        setLoaded({ regions, refNameAliases, cytobands, }: {
             regions: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
-            lowerCaseRefNameAliases: {
-                [x: string]: string;
-            };
             cytobands: import("../util").Feature[];
         }): void;
         setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCaseAliases: {
-            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         setLoadingP(p?: Promise<void>): void;
@@ -359,6 +338,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string;
         }>;
+        afterCreate(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
     readonly assemblyNamesList: any[];
     readonly assemblyList: AnyConfigurationModel[];
@@ -373,18 +353,18 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         refNameAliases: {
             [x: string]: string;
         } | undefined;
-        lowerCaseRefNameAliases: {
-            [x: string]: string;
-        } | undefined;
         cytobands: import("../util").Feature[] | undefined;
     } & {
         getConf(arg: string): any;
+        readonly lowerCaseRefNameAliases: {
+            [k: string]: string;
+        } | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
         readonly regions: import("./assembly").BasicRegion[] | undefined;
         readonly aliases: string[];
-        readonly displayName: string | undefined;
+        readonly displayName: string;
         hasName(name: string): boolean;
         readonly allAliases: string[];
         readonly allRefNames: string[] | undefined;
@@ -399,22 +379,17 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
+        setLoaded({ regions, refNameAliases, cytobands, }: {
             regions: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
-            lowerCaseRefNameAliases: {
-                [x: string]: string;
-            };
             cytobands: import("../util").Feature[];
         }): void;
         setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCaseAliases: {
-            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         setLoadingP(p?: Promise<void>): void;
@@ -434,6 +409,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string;
         }>;
+        afterCreate(): void;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
     }, {
@@ -443,18 +419,18 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         refNameAliases: {
             [x: string]: string;
         } | undefined;
-        lowerCaseRefNameAliases: {
-            [x: string]: string;
-        } | undefined;
         cytobands: import("../util").Feature[] | undefined;
     } & {
         getConf(arg: string): any;
+        readonly lowerCaseRefNameAliases: {
+            [k: string]: string;
+        } | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
         readonly regions: import("./assembly").BasicRegion[] | undefined;
         readonly aliases: string[];
-        readonly displayName: string | undefined;
+        readonly displayName: string;
         hasName(name: string): boolean;
         readonly allAliases: string[];
         readonly allRefNames: string[] | undefined;
@@ -469,22 +445,17 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
+        setLoaded({ regions, refNameAliases, cytobands, }: {
             regions: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
-            lowerCaseRefNameAliases: {
-                [x: string]: string;
-            };
             cytobands: import("../util").Feature[];
         }): void;
         setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCaseAliases: {
-            [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         setLoadingP(p?: Promise<void>): void;
@@ -504,6 +475,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string;
         }>;
+        afterCreate(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
     getRefNameMapForAdapter(adapterConf: AdapterConf, assemblyName: string | undefined, opts: {
         stopToken?: string;

package/data_adapters/dataAdapterCache.d.ts

@@ -9,6 +9,6 @@ interface AdapterCacheEntry {
 }
 export declare function getAdapter(pluginManager: PluginManager, sessionId: string, adapterConfigSnapshot: SnapshotIn<AnyConfigurationSchemaType>): Promise<AdapterCacheEntry>;
 export type getSubAdapterType = (adapterConfigSnap: ConfigSnap) => ReturnType<typeof getAdapter>;
-export declare function freeAdapterResources(args: Record<string, any>): void;
+export declare function freeAdapterResources(args: Record<string, any>): Promise<void>;
 export declare function clearAdapterCache(): void;
 export {};

package/data_adapters/dataAdapterCache.js

@@ -5,35 +5,38 @@ exports.freeAdapterResources = freeAdapterResources;
 exports.clearAdapterCache = clearAdapterCache;
 const util_1 = require("./util");
 let adapterCache = {};
+async function getAdapterPre(pluginManager, sessionId, adapterConfigSnapshot) {
+    const adapterType = adapterConfigSnapshot === null || adapterConfigSnapshot === void 0 ? void 0 : adapterConfigSnapshot.type;
+    if (!adapterType) {
+        throw new Error(`could not determine adapter type from adapter config snapshot ${JSON.stringify(adapterConfigSnapshot)}`);
+    }
+    const dataAdapterType = pluginManager.getAdapterType(adapterType);
+    if (!dataAdapterType) {
+        throw new Error(`unknown data adapter type ${adapterType}`);
+    }
+    const adapterConfig = dataAdapterType.configSchema.create(adapterConfigSnapshot, { pluginManager });
+    const getSubAdapter = getAdapter.bind(null, pluginManager, sessionId);
+    const CLASS = await dataAdapterType.getAdapterClass();
+    const dataAdapter = new CLASS(adapterConfig, getSubAdapter, pluginManager);
+    return {
+        dataAdapter,
+        sessionIds: new Set([sessionId]),
+    };
+}
 async function getAdapter(pluginManager, sessionId, adapterConfigSnapshot) {
+    var _a;
     const cacheKey = (0, util_1.adapterConfigCacheKey)(adapterConfigSnapshot);
-    if (!adapterCache[cacheKey]) {
-        const adapterType = adapterConfigSnapshot === null || adapterConfigSnapshot === void 0 ? void 0 : adapterConfigSnapshot.type;
-        if (!adapterType) {
-            throw new Error(`could not determine adapter type from adapter config snapshot ${JSON.stringify(adapterConfigSnapshot)}`);
-        }
-        const dataAdapterType = pluginManager.getAdapterType(adapterType);
-        if (!dataAdapterType) {
-            throw new Error(`unknown data adapter type ${adapterType}`);
-        }
-        const adapterConfig = dataAdapterType.configSchema.create(adapterConfigSnapshot, { pluginManager });
-        const getSubAdapter = getAdapter.bind(null, pluginManager, sessionId);
-        const CLASS = await dataAdapterType.getAdapterClass();
-        const dataAdapter = new CLASS(adapterConfig, getSubAdapter, pluginManager);
-        adapterCache[cacheKey] = {
-            dataAdapter,
-            sessionIds: new Set([sessionId]),
-        };
-    }
-    const cacheEntry = adapterCache[cacheKey];
-    cacheEntry.sessionIds.add(sessionId);
-    return cacheEntry;
+    (_a = adapterCache[cacheKey]) !== null && _a !== void 0 ? _a : (adapterCache[cacheKey] = getAdapterPre(pluginManager, sessionId, adapterConfigSnapshot));
+    const ret = await adapterCache[cacheKey];
+    ret.sessionIds.add(sessionId);
+    return ret;
 }
-function freeAdapterResources(args) {
+async function freeAdapterResources(args) {
     const specKeys = Object.keys(args);
     if (specKeys.length === 1 && specKeys[0] === 'sessionId') {
         const { sessionId } = args;
-        for (const [cacheKey, cacheEntry] of Object.entries(adapterCache)) {
+        for (const [cacheKey, cacheEntryP] of Object.entries(adapterCache)) {
+            const cacheEntry = await cacheEntryP;
             cacheEntry.sessionIds.delete(sessionId);
             if (cacheEntry.sessionIds.size === 0) {
                 delete adapterCache[cacheKey];
@@ -41,7 +44,8 @@ function freeAdapterResources(args) {
         }
     }
     else {
-        for (const cacheEntry of Object.values(adapterCache)) {
+        for (const cacheEntryP of Object.values(adapterCache)) {
+            const cacheEntry = await cacheEntryP;
             const regions = args.regions || (args.region ? [args.region] : []);
             for (const region of regions) {
                 if (region.refName !== undefined) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "3.5.0",
+  "version": "3.5.1",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -51,7 +51,6 @@
     "jexl": "^2.3.0",
     "librpc-web-mod": "^1.1.5",
     "load-script": "^2.0.0",
-    "material-ui-popup-state": "^5.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
@@ -70,5 +69,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "8a8aa0aab2229dece106a5715a767e649e2fe92b"
+  "gitHead": "cb8859da9d838ad2594964777c5c54f385d98f5e"
 }

package/rpc/methods/CoreFreeResources.js

@@ -11,7 +11,7 @@ class CoreFreeResources extends RpcMethodType_1.default {
         this.name = 'CoreFreeResources';
     }
     async execute(args) {
-        (0, dataAdapterCache_1.freeAdapterResources)(args);
+        await (0, dataAdapterCache_1.freeAdapterResources)(args);
         for (const renderer of this.pluginManager.getRendererTypes()) {
             renderer.freeResources(args);
         }