@jbrowse/plugin-legacy-jbrowse 3.6.5 → 4.0.0

package/esm/JBrowse1Connection/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const JBrowse1Connection: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const JBrowse1Connection: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     dataDirLocation: {
         type: string;
         defaultValue: {
@@ -12,7 +12,7 @@ declare const JBrowse1Connection: import("@jbrowse/core/configuration/configurat
         type: string;
         defaultValue: never[];
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     name: {
         type: string;
         defaultValue: string;
@@ -23,5 +23,5 @@ declare const JBrowse1Connection: import("@jbrowse/core/configuration/configurat
         defaultValue: never[];
         description: string;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
 export default JBrowse1Connection;

package/esm/JBrowse1Connection/get-value.d.ts

@@ -0,0 +1,10 @@
+export interface Options {
+    default?: unknown;
+    separator?: string;
+    joinChar?: string;
+    join?: (segs: string[]) => string;
+    split?: (path: string) => string[];
+    isValid?: (key: string, target: {}) => boolean;
+}
+declare const getValue: (target: unknown, path: string | number | string[], options?: Options) => unknown;
+export default getValue;

package/esm/JBrowse1Connection/get-value.js

@@ -0,0 +1,84 @@
+const isObject = v => v !== null && typeof v === 'object';
+const join = (segs, joinChar, options) => {
+    if (typeof options.join === 'function') {
+        return options.join(segs);
+    }
+    return segs[0] + joinChar + segs[1];
+};
+const split = (path, splitChar, options) => {
+    if (typeof options.split === 'function') {
+        return options.split(path);
+    }
+    return path.split(splitChar);
+};
+const isValid = (key, target = {}, options) => {
+    if (typeof options?.isValid === 'function') {
+        return options.isValid(key, target);
+    }
+    return true;
+};
+const isValidObject = (v) => {
+    return isObject(v) || typeof v === 'function';
+};
+const getValue = (target, path, options = {}) => {
+    if (!isObject(options)) {
+        options = { default: options };
+    }
+    if (!isValidObject(target)) {
+        return options.default !== undefined ? options.default : target;
+    }
+    if (typeof path === 'number') {
+        path = String(path);
+    }
+    const pathIsArray = Array.isArray(path);
+    const pathIsString = typeof path === 'string';
+    const splitChar = options.separator || '.';
+    const joinChar = options.joinChar || (typeof splitChar === 'string' ? splitChar : '.');
+    if (!pathIsString && !pathIsArray) {
+        return target;
+    }
+    if (target[path] !== undefined) {
+        return isValid(path, target, options) ? target[path] : options.default;
+    }
+    const segs = pathIsArray ? path : split(path, splitChar, options);
+    const len = segs.length;
+    let idx = 0;
+    do {
+        let prop = segs[idx];
+        if (typeof prop !== 'string') {
+            prop = String(prop);
+        }
+        while (prop.endsWith('\\')) {
+            prop = join([prop.slice(0, -1), segs[++idx] || ''], joinChar, options);
+        }
+        if (target[prop] !== undefined) {
+            if (!isValid(prop, target, options)) {
+                return options.default;
+            }
+            target = target[prop];
+        }
+        else {
+            let hasProp = false;
+            let n = idx + 1;
+            while (n < len) {
+                prop = join([prop, segs[n++]], joinChar, options);
+                if ((hasProp = target[prop] !== undefined)) {
+                    if (!isValid(prop, target, options)) {
+                        return options.default;
+                    }
+                    target = target[prop];
+                    idx = n - 1;
+                    break;
+                }
+            }
+            if (!hasProp) {
+                return options.default;
+            }
+        }
+    } while (++idx < len && isValidObject(target));
+    if (idx === len) {
+        return target;
+    }
+    return options.default;
+};
+export default getValue;

package/esm/JBrowse1Connection/index.js

@@ -1,6 +1,6 @@
 import ConnectionType from '@jbrowse/core/pluggableElementTypes/ConnectionType';
-import configSchema from './configSchema';
-import modelFactory from './model';
+import configSchema from "./configSchema.js";
+import modelFactory from "./model.js";
 export default function JBrowse1ConnectionF(pluginManager) {
     pluginManager.addConnectionType(() => new ConnectionType({
         name: 'JBrowse1Connection',

package/esm/JBrowse1Connection/jb1ConfigLoad.d.ts

@@ -1,4 +1,4 @@
-import type { Config, JBLocation } from './types';
+import type { Config, JBLocation } from './types.ts';
 export declare function fetchJb1(dataRoot?: JBLocation, baseConfig?: Config, baseConfigRoot?: JBLocation): Promise<Config>;
 export declare function createFinalConfig(baseConfig: Config, defaults?: {
     tracks: never[];

package/esm/JBrowse1Connection/jb1ConfigLoad.js

@@ -1,6 +1,6 @@
 import { openLocation } from '@jbrowse/core/util/io';
-import { parseJB1Conf, parseJB1Json, regularizeConf } from './jb1ConfigParse';
-import { deepUpdate, fillTemplate } from './util';
+import { parseJB1Conf, parseJB1Json, regularizeConf } from "./jb1ConfigParse.js";
+import { deepUpdate, fillTemplate } from "./util.js";
 function isUriLocation(location) {
     return location.uri !== undefined;
 }

package/esm/JBrowse1Connection/jb1ConfigParse.d.ts

@@ -1,4 +1,4 @@
-import type { Config } from './types';
+import type { Config } from './types.ts';
 export declare function parseJB1Json(config: Config | string, url: string): Config;
 export declare function parseJB1Conf(config: string, url: string): Config;
 export declare function regularizeConf(conf: Config, url: string): Config;

package/esm/JBrowse1Connection/jb1ConfigParse.js

@@ -1,7 +1,7 @@
 import { objectHash } from '@jbrowse/core/util';
-import getValue from 'get-value';
 import setValue from 'set-value';
-import { isSource, isTrack } from './util';
+import getValue from "./get-value.js";
+import { isSource, isTrack } from "./util.js";
 export function parseJB1Json(config, url) {
     if (typeof config === 'string') {
         let parsedConf;
@@ -143,7 +143,7 @@ export function regularizeConf(conf, url) {
         }
     }
     const meta = conf.trackMetadata;
-    if (meta === null || meta === void 0 ? void 0 : meta.sources) {
+    if (meta?.sources) {
         if (typeof meta.sources === 'string') {
             meta.sources = [meta.sources];
         }
@@ -184,10 +184,14 @@ export function regularizeConf(conf, url) {
     if (conf.sourceUrl) {
         const addBase = [];
         if (conf.tracks) {
-            addBase.push(...conf.tracks);
+            for (const track of conf.tracks) {
+                addBase.push(track);
+            }
         }
         if (conf.stores) {
-            addBase.push(...Object.values(conf.stores));
+            for (const store of Object.values(conf.stores)) {
+                addBase.push(store);
+            }
         }
         if (conf.names) {
             addBase.push(conf.names);
@@ -252,11 +256,10 @@ function regularizeClass(root, className) {
     return className;
 }
 function guessStoreClass(trackConfig, urlTemplate) {
-    var _a, _b;
     if (!trackConfig) {
         return '';
     }
-    if ((_a = trackConfig.type) === null || _a === void 0 ? void 0 : _a.includes('/FixedImage')) {
+    if (trackConfig.type?.includes('/FixedImage')) {
         return `JBrowse/Store/TiledImage/Fixed${trackConfig.backendVersion === 0 ? '_v0' : ''}`;
     }
     if (/\.jsonz?$/i.test(urlTemplate)) {
@@ -298,13 +301,12 @@ function guessStoreClass(trackConfig, urlTemplate) {
     if (/\.2bit$/i.test(urlTemplate)) {
         return 'JBrowse/Store/SeqFeature/TwoBit';
     }
-    if ((_b = trackConfig.type) === null || _b === void 0 ? void 0 : _b.endsWith('/Sequence')) {
+    if (trackConfig.type?.endsWith('/Sequence')) {
         return 'JBrowse/Store/Sequence/StaticChunked';
     }
     return '';
 }
 function synthesizeTrackStoreConfig(mainConf, trackConfig) {
-    var _a;
     const { urlTemplate = '' } = trackConfig;
     const storeClass = trackConfig.storeClass
         ? regularizeClass('JBrowse/Store', trackConfig.storeClass)
@@ -322,7 +324,7 @@ function synthesizeTrackStoreConfig(mainConf, trackConfig) {
             storeClass === 'JBrowse/Store/SeqFeature/TwoBit' ||
             storeClass === 'JBrowse/Store/Sequence/TwoBit' ||
             trackConfig.useAsRefSeqStore) &&
-            !((_a = mainConf.stores) === null || _a === void 0 ? void 0 : _a.refseqs)
+            !mainConf.stores?.refseqs
             ? 'refseqs'
             : `store${objectHash(storeConf)}`;
     if (!mainConf.stores) {

package/esm/JBrowse1Connection/jb1ToJb2.d.ts

@@ -1,4 +1,4 @@
-import type { RefSeqs, Track } from './types';
+import type { RefSeqs, Track } from './types.ts';
 interface Jb2Track {
     trackId: string;
     name: string;
@@ -30,7 +30,6 @@ interface Jb2Adapter {
         indexType?: string;
     };
     rootUrlTemplate?: Jb2Location;
-    sequenceAdapter?: Jb2Adapter;
 }
 interface Jb2Feature {
     refName: string;
@@ -44,6 +43,6 @@ interface Jb2Location {
     blobId?: string;
     locationType?: string;
 }
-export declare function convertTrackConfig(jb1TrackConfig: Track, dataRoot: string, sequenceAdapter: Jb2Adapter): Jb2Track;
+export declare function convertTrackConfig(jb1TrackConfig: Track, dataRoot: string): Jb2Track;
 export declare function createRefSeqsAdapter(refSeqs: string | RefSeqs): Promise<Jb2Adapter>;
 export {};

package/esm/JBrowse1Connection/jb1ToJb2.js

@@ -1,8 +1,7 @@
 import { objectHash } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { UNKNOWN, UNSUPPORTED, generateUnknownTrackConf, generateUnsupportedTrackConf, guessAdapter, guessTrackType, } from '@jbrowse/core/util/tracks';
-export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
-    var _a, _b, _c, _d, _e;
+export function convertTrackConfig(jb1TrackConfig, dataRoot) {
     const jb2TrackConfig = {
         trackId: objectHash(jb1TrackConfig),
         name: jb1TrackConfig.key || jb1TrackConfig.label,
@@ -12,11 +11,11 @@ export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
     if (description) {
         jb2TrackConfig.description = description;
     }
-    const category = jb1TrackConfig.category || ((_a = jb1TrackConfig.metadata) === null || _a === void 0 ? void 0 : _a.category);
+    const category = jb1TrackConfig.category || jb1TrackConfig.metadata?.category;
     jb2TrackConfig.category = category ? category.split(/\s*\/\s*/) : [];
     const { storeClass } = jb1TrackConfig;
     if (!jb1TrackConfig.urlTemplate) {
-        if (!(storeClass === null || storeClass === void 0 ? void 0 : storeClass.endsWith('FromConfig'))) {
+        if (!storeClass?.endsWith('FromConfig')) {
             const trackIdentifier = jb1TrackConfig.key || jb1TrackConfig.label;
             console.warn(`Could not import JBrowse1 track "${trackIdentifier}" because it does not have a "urlTemplate" or is not a "FromConfig" track`);
             return generateUnsupportedTrackConf(jb2TrackConfig.name, trackIdentifier, jb2TrackConfig.category);
@@ -67,17 +66,16 @@ export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
             const adapter = {
                 type: 'CramAdapter',
                 cramLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                sequenceAdapter,
+                craiLocation: jb1TrackConfig.craiUrlTemplate
+                    ? {
+                        uri: resolveUrlTemplate(jb1TrackConfig.craiUrlTemplate),
+                        locationType: 'UriLocation',
+                    }
+                    : {
+                        uri: `${urlTemplate}.crai`,
+                        locationType: 'UriLocation',
+                    },
             };
-            adapter.craiLocation = jb1TrackConfig.craiUrlTemplate
-                ? {
-                    uri: resolveUrlTemplate(jb1TrackConfig.craiUrlTemplate),
-                    locationType: 'UriLocation',
-                }
-                : {
-                    uri: `${urlTemplate}.crai`,
-                    locationType: 'UriLocation',
-                };
             return {
                 ...jb2TrackConfig,
                 type: 'AlignmentsTrack',
@@ -96,10 +94,10 @@ export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/BigWig' ||
             storeClass === 'JBrowse/Store/BigWig') {
-            if ((_b = jb1TrackConfig.type) === null || _b === void 0 ? void 0 : _b.endsWith('XYPlot')) {
+            if (jb1TrackConfig.type?.endsWith('XYPlot')) {
                 jb2TrackConfig.defaultRendering = 'xyplot';
             }
-            else if ((_c = jb1TrackConfig.type) === null || _c === void 0 ? void 0 : _c.endsWith('Density')) {
+            else if (jb1TrackConfig.type?.endsWith('Density')) {
                 jb2TrackConfig.defaultRendering = 'density';
             }
             return {
@@ -257,16 +255,16 @@ export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
             const adapter = {
                 type: 'IndexedFastaAdapter',
                 fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+                faiLocation: jb1TrackConfig.faiUrlTemplate
+                    ? {
+                        uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
+                        locationType: 'UriLocation',
+                    }
+                    : {
+                        uri: `${urlTemplate}.fai`,
+                        locationType: 'UriLocation',
+                    },
             };
-            adapter.faiLocation = jb1TrackConfig.faiUrlTemplate
-                ? {
-                    uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
-                    locationType: 'UriLocation',
-                }
-                : {
-                    uri: `${urlTemplate}.fai`,
-                    locationType: 'UriLocation',
-                };
             return {
                 ...jb2TrackConfig,
                 type: 'SequenceTrack',
@@ -277,25 +275,25 @@ export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
             const adapter = {
                 type: 'BgzipFastaAdapter',
                 fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+                faiLocation: jb1TrackConfig.faiUrlTemplate
+                    ? {
+                        uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
+                        locationType: 'UriLocation',
+                    }
+                    : {
+                        uri: `${urlTemplate}.fai`,
+                        locationType: 'UriLocation',
+                    },
+                gziLocation: jb1TrackConfig.gziUrlTemplate
+                    ? {
+                        uri: resolveUrlTemplate(jb1TrackConfig.gziUrlTemplate),
+                        locationType: 'UriLocation',
+                    }
+                    : {
+                        uri: `${urlTemplate}.gzi`,
+                        locationType: 'UriLocation',
+                    },
             };
-            adapter.faiLocation = jb1TrackConfig.faiUrlTemplate
-                ? {
-                    uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
-                    locationType: 'UriLocation',
-                }
-                : {
-                    uri: `${urlTemplate}.fai`,
-                    locationType: 'UriLocation',
-                };
-            adapter.gziLocation = jb1TrackConfig.gziUrlTemplate
-                ? {
-                    uri: resolveUrlTemplate(jb1TrackConfig.gziUrlTemplate),
-                    locationType: 'UriLocation',
-                }
-                : {
-                    uri: `${urlTemplate}.gzi`,
-                    locationType: 'UriLocation',
-                };
             return {
                 ...jb2TrackConfig,
                 type: 'ReferenceSequenceTrack',
@@ -322,10 +320,10 @@ export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
     }
     jb2TrackConfig.type = guessTrackType(jb2TrackConfig.adapter.type);
     if (jb2TrackConfig.type === 'QuantitativeTrack') {
-        if ((_d = jb1TrackConfig.type) === null || _d === void 0 ? void 0 : _d.endsWith('XYPlot')) {
+        if (jb1TrackConfig.type?.endsWith('XYPlot')) {
             jb2TrackConfig.defaultRendering = 'xyplot';
         }
-        else if ((_e = jb1TrackConfig.type) === null || _e === void 0 ? void 0 : _e.endsWith('Density')) {
+        else if (jb1TrackConfig.type?.endsWith('Density')) {
             jb2TrackConfig.defaultRendering = 'density';
         }
     }

package/esm/JBrowse1Connection/model.d.ts

@@ -1,8 +1,8 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-export default function stateModelFactory(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<{
+export default function stateModelFactory(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
+    name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
+    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
         name: {
             type: string;
             defaultValue: string;
@@ -13,9 +13,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             defaultValue: never[];
             description: string;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "connectionId">>;
 } & {
-    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
         dataDirLocation: {
             type: string;
             defaultValue: {
@@ -29,7 +29,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             type: string;
             defaultValue: never[];
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
         name: {
             type: string;
             defaultValue: string;
@@ -40,36 +40,28 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             defaultValue: never[];
             description: string;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
-    type: import("mobx-state-tree").ISimpleType<"JBrowse1Connection">;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"JBrowse1Connection">;
 }, {
     connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
 } & {
     afterAttach(): void;
     addTrackConf(trackConf: Record<string, unknown> | ({
         [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
             [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
     addTrackConfs(trackConfs: (Record<string, unknown> | ({
         [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
             [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
     setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
     clear(): void;
 } & {
     connect(): Promise<void>;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;

package/esm/JBrowse1Connection/model.js

@@ -1,8 +1,8 @@
-import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/configuration';
+import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
 import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models';
 import { getSession } from '@jbrowse/core/util';
-import { types } from 'mobx-state-tree';
-import configSchema from './configSchema';
+import { types } from '@jbrowse/mobx-state-tree';
+import configSchema from "./configSchema.js";
 export default function stateModelFactory(pluginManager) {
     return types
         .compose('JBrowse1Connection', BaseConnectionModelFactory(pluginManager), types.model({
@@ -11,24 +11,18 @@ export default function stateModelFactory(pluginManager) {
     }))
         .actions(self => ({
         async connect() {
-            var _a, _b;
             const session = getSession(self);
             try {
                 const dataDirLocation = getConf(self, 'dataDirLocation');
-                const { fetchJb1 } = await import('./jb1ConfigLoad');
-                const { convertTrackConfig } = await import('./jb1ToJb2');
+                const { fetchJb1 } = await import("./jb1ConfigLoad.js");
+                const { convertTrackConfig } = await import("./jb1ToJb2.js");
                 const config = await fetchJb1(dataDirLocation);
                 const assemblyName = getConf(self, 'assemblyNames')[0];
                 if (!assemblyName) {
                     throw new Error('assembly name required for JBrowse 1 connection');
                 }
-                const conf = session.assemblies.find(a => readConfObject(a, 'name') === assemblyName);
-                if (!conf) {
-                    throw new Error(`Assembly "${assemblyName}" not found`);
-                }
-                const sequenceAdapter = readConfObject(conf, ['sequence', 'adapter']);
-                const jb2Tracks = (_a = config.tracks) === null || _a === void 0 ? void 0 : _a.map(jb1Track => ({
-                    ...convertTrackConfig(jb1Track, config.dataRoot || '', sequenceAdapter),
+                const jb2Tracks = config.tracks?.map(jb1Track => ({
+                    ...convertTrackConfig(jb1Track, config.dataRoot || ''),
                     assemblyNames: [assemblyName],
                 }));
                 self.setTrackConfs(jb2Tracks);
@@ -36,7 +30,7 @@ export default function stateModelFactory(pluginManager) {
             catch (error) {
                 console.error(error);
                 session.notifyError(`There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`, error);
-                (_b = session.breakConnection) === null || _b === void 0 ? void 0 : _b.call(session, self.configuration);
+                session.breakConnection?.(self.configuration);
             }
         },
     }));

package/esm/JBrowse1Connection/util.d.ts

@@ -1,4 +1,4 @@
-import type { Source, Track } from './types';
+import type { Source, Track } from './types.ts';
 export declare function isTrack(arg: any): arg is Track;
 export declare function isSource(arg: any): arg is Source;
 type Obj = Record<string, any>;

package/esm/JBrowse1Connection/util.js

@@ -1,12 +1,17 @@
-import getValue from 'get-value';
+import getValue from "./get-value.js";
 export function isTrack(arg) {
-    return (arg === null || arg === void 0 ? void 0 : arg.label) && typeof arg.label === 'string';
+    return arg?.label && typeof arg.label === 'string';
 }
 export function isSource(arg) {
-    return (arg === null || arg === void 0 ? void 0 : arg.url) && typeof arg.url === 'string';
+    return arg?.url && typeof arg.url === 'string';
 }
 export function deepUpdate(a, b) {
     for (const prop of Object.keys(b)) {
+        if (prop === '__proto__' ||
+            prop === 'constructor' ||
+            prop === 'prototype') {
+            continue;
+        }
         if (prop in a &&
             typeof b[prop] === 'object' &&
             typeof a[prop] === 'object') {
@@ -66,6 +71,11 @@ export function structuredClone(src) {
 function mixin(dest, source, copyFunc) {
     const empty = {};
     for (const name in source) {
+        if (name === '__proto__' ||
+            name === 'constructor' ||
+            name === 'prototype') {
+            continue;
+        }
         const s = source[name];
         if (!(name in dest) ||
             (dest[name] !== s && (!(name in empty) || empty[name] !== s))) {

package/esm/JBrowse1TextSearchAdapter/HttpMap.js

@@ -1,5 +1,20 @@
-import crc32 from 'crc/crc32';
+const crcTable = new Uint32Array(256);
+for (let i = 0; i < 256; i++) {
+    let c = i;
+    for (let j = 0; j < 8; j++) {
+        c = c & 1 ? 0xedb88320 ^ (c >>> 1) : c >>> 1;
+    }
+    crcTable[i] = c;
+}
+function crc32(str) {
+    let crc = 0xffffffff;
+    for (let i = 0; i < str.length; i++) {
+        crc = crcTable[(crc ^ str.charCodeAt(i)) & 0xff] ^ (crc >>> 8);
+    }
+    return (crc ^ 0xffffffff) >>> 0;
+}
 export default class HttpMap {
+    url;
     constructor(args) {
         this.url = args.url.endsWith('/') ? args.url : `${args.url}/`;
     }

package/esm/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.d.ts

@@ -1,6 +1,6 @@
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import HttpMap from './HttpMap';
+import HttpMap from './HttpMap.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { BaseTextSearchAdapter, BaseTextSearchArgs } from '@jbrowse/core/data_adapters/BaseAdapter';

package/esm/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.js

@@ -1,8 +1,10 @@
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 import { readConfObject } from '@jbrowse/core/configuration';
 import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import HttpMap from './HttpMap';
+import HttpMap from "./HttpMap.js";
 export default class JBrowse1TextSearchAdapter extends BaseAdapter {
+    httpMap;
+    tracksNames;
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
         const namesIndex = readConfObject(config, 'namesIndexLocation');

package/esm/JBrowse1TextSearchAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const _default: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const _default: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     namesIndexLocation: {
         type: string;
         defaultValue: {
@@ -17,5 +17,5 @@ declare const _default: import("@jbrowse/core/configuration/configurationSchema"
         defaultValue: never[];
         description: string;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "textSearchAdapterId">>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "textSearchAdapterId">>;
 export default _default;

package/esm/JBrowse1TextSearchAdapter/index.js

@@ -1,10 +1,10 @@
 import TextSearchAdapterType from '@jbrowse/core/pluggableElementTypes/TextSearchAdapterType';
-import configSchema from './configSchema';
+import configSchema from "./configSchema.js";
 export default function JBrowse1TextSearchAdapterF(pluginManager) {
     pluginManager.addTextSearchAdapterType(() => new TextSearchAdapterType({
         name: 'JBrowse1TextSearchAdapter',
         configSchema,
         description: 'A JBrowse 1 text search adapter',
-        getAdapterClass: () => import('./JBrowse1TextSearchAdapter').then(t => t.default),
+        getAdapterClass: () => import("./JBrowse1TextSearchAdapter.js").then(t => t.default),
     }));
 }

package/esm/NCListAdapter/NCListAdapter.d.ts

@@ -1,5 +1,5 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import NCListFeature from './NCListFeature';
+import NCListFeature from './NCListFeature.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';