@jbrowse/plugin-legacy-jbrowse 2.6.2 → 2.7.0

package/dist/JBrowse1Connection/jb1ConfigParse.js

@@ -170,7 +170,7 @@ function regularizeConf(conf, url) {
     }
     // regularize trackMetadata.sources
     const meta = conf.trackMetadata;
-    if (meta && meta.sources) {
+    if (meta === null || meta === void 0 ? void 0 : meta.sources) {
         // if it's a single source config, wrap it in an arrayref
         if (typeof meta.sources === 'string') {
             meta.sources = [meta.sources];
@@ -344,6 +344,7 @@ function guessStoreClass(trackConfig, urlTemplate) {
     return '';
 }
 function synthesizeTrackStoreConfig(mainConf, trackConfig) {
+    var _a;
     // figure out what data store class to use with the track, applying some
     // defaults if it is not explicit in the configuration
     const { urlTemplate = '' } = trackConfig;
@@ -366,7 +367,7 @@ function synthesizeTrackStoreConfig(mainConf, trackConfig) {
             storeClass === 'JBrowse/Store/SeqFeature/TwoBit' ||
             storeClass === 'JBrowse/Store/Sequence/TwoBit' ||
             trackConfig.useAsRefSeqStore) &&
-            !(mainConf.stores && mainConf.stores.refseqs)
+            !((_a = mainConf.stores) === null || _a === void 0 ? void 0 : _a.refseqs)
             ? 'refseqs'
             : `store${(0, util_1.objectHash)(storeConf)}`;
     // record it

package/dist/JBrowse1Connection/jb1ToJb2.js

@@ -5,6 +5,7 @@ const io_1 = require("@jbrowse/core/util/io");
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
 function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
+    var _a;
     const jb2TrackConfig = {
         trackId: (0, util_1.objectHash)(jb1TrackConfig),
         name: jb1TrackConfig.key || jb1TrackConfig.label,
@@ -14,8 +15,7 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
     if (description) {
         jb2TrackConfig.description = description;
     }
-    const category = jb1TrackConfig.category ||
-        (jb1TrackConfig.metadata && jb1TrackConfig.metadata.category);
+    const category = jb1TrackConfig.category || ((_a = jb1TrackConfig.metadata) === null || _a === void 0 ? void 0 : _a.category);
     jb2TrackConfig.category = category ? category.split(/\s*\/\s*/) : [];
     const { storeClass } = jb1TrackConfig;
     if (!jb1TrackConfig.urlTemplate) {

package/dist/JBrowse1Connection/model.js

@@ -40,7 +40,7 @@ function default_1(pluginManager) {
     }))
         .actions(self => ({
         async connect() {
-            var _a;
+            var _a, _b;
             const session = (0, util_1.getSession)(self);
             try {
                 const dataDirLocation = (0, configuration_1.getConf)(self, 'dataDirLocation');
@@ -51,14 +51,11 @@ function default_1(pluginManager) {
                 if (!assemblyName) {
                     throw new Error('assembly name required for JBrowse 1 connection');
                 }
-                const assemblyConf = session.assemblies.find(a => (0, configuration_1.readConfObject)(a, 'name') === assemblyName);
-                if (!assemblyConf) {
+                const conf = session.assemblies.find(a => (0, configuration_1.readConfObject)(a, 'name') === assemblyName);
+                if (!conf) {
                     throw new Error(`Assembly "${assemblyName}" not found`);
                 }
-                const sequenceAdapter = (0, configuration_1.readConfObject)(assemblyConf, [
-                    'sequence',
-                    'adapter',
-                ]);
+                const sequenceAdapter = (0, configuration_1.readConfObject)(conf, ['sequence', 'adapter']);
                 // @ts-expect-error
                 const jb2Tracks = (_a = config.tracks) === null || _a === void 0 ? void 0 : _a.map(jb1Track => ({
                     ...convertTrackConfig(jb1Track, config.dataRoot || '', sequenceAdapter),
@@ -69,7 +66,7 @@ function default_1(pluginManager) {
             catch (error) {
                 console.error(error);
                 session.notify(`There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`, 'error');
-                session.breakConnection(self.configuration);
+                (_b = session.breakConnection) === null || _b === void 0 ? void 0 : _b.call(session, self.configuration);
             }
         },
     }));

package/dist/JBrowse1Connection/util.js

@@ -7,12 +7,12 @@ exports.clone = exports.fillTemplate = exports.deepUpdate = exports.isSource = e
 const get_value_1 = __importDefault(require("get-value"));
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function isTrack(arg) {
-    return arg && arg.label && typeof arg.label === 'string';
+    return (arg === null || arg === void 0 ? void 0 : arg.label) && typeof arg.label === 'string';
 }
 exports.isTrack = isTrack;
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function isSource(arg) {
-    return arg && arg.url && typeof arg.url === 'string';
+    return (arg === null || arg === void 0 ? void 0 : arg.url) && typeof arg.url === 'string';
 }
 exports.isSource = isSource;
 function deepUpdate(a, b) {

package/dist/JBrowse1TextSearchAdapter/HttpMap.js

@@ -11,7 +11,7 @@ const buffer_crc32_1 = __importDefault(require("buffer-crc32"));
 class HttpMap {
     constructor(args) {
         // make sure url has a trailing slash
-        this.url = /\/$/.test(args.url) ? args.url : `${args.url}/`;
+        this.url = args.url.endsWith('/') ? args.url : `${args.url}/`;
     }
     /**
      * loads meta.json file from names directory and reads number of hash_bits used

package/dist/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.d.ts

@@ -14,7 +14,7 @@ interface SearchResults {
     } | string)[];
     exact: [string, number, string, string, number, number][];
 }
-export type NamesIndexRecord = string | Array<string | number>;
+export type NamesIndexRecord = string | (string | number)[];
 type IndexFile = Record<string, SearchResults>;
 export default class JBrowse1TextSearchAdapter extends BaseAdapter implements BaseTextSearchAdapter {
     httpMap: HttpMap;

package/dist/NCListAdapter/NCListAdapter.js

@@ -46,8 +46,9 @@ class NCListAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return new NCListFeature_1.default(ncFeature, undefined, `${this.id}-${ncFeature.id()}`);
     }
     async hasDataForRefName(refName) {
+        var _a;
         const root = await this.nclist.getDataRoot(refName);
-        return !!(root && root.stats && root.stats.featureCount);
+        return !!((_a = root === null || root === void 0 ? void 0 : root.stats) === null || _a === void 0 ? void 0 : _a.featureCount);
     }
     /**
      * NCList is unable to get list of ref names so returns empty

package/dist/NCListAdapter/NCListFeature.js

@@ -6,8 +6,9 @@ const jb1ToJb2 = { seq_id: 'refName' };
  * wrapper to adapt nclist features to act like jbrowse 2 features
  */
 class NCListFeature {
+    constructor(
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    constructor(ncFeature, parent, id) {
+    ncFeature, parent, id) {
         this.ncFeature = ncFeature;
         this.uniqueId = id || ncFeature.id();
         this.parentHandle = parent;

package/esm/JBrowse1Connection/jb1ConfigParse.js

@@ -162,7 +162,7 @@ export function regularizeConf(conf, url) {
     }
     // regularize trackMetadata.sources
     const meta = conf.trackMetadata;
-    if (meta && meta.sources) {
+    if (meta === null || meta === void 0 ? void 0 : meta.sources) {
         // if it's a single source config, wrap it in an arrayref
         if (typeof meta.sources === 'string') {
             meta.sources = [meta.sources];
@@ -335,6 +335,7 @@ function guessStoreClass(trackConfig, urlTemplate) {
     return '';
 }
 function synthesizeTrackStoreConfig(mainConf, trackConfig) {
+    var _a;
     // figure out what data store class to use with the track, applying some
     // defaults if it is not explicit in the configuration
     const { urlTemplate = '' } = trackConfig;
@@ -357,7 +358,7 @@ function synthesizeTrackStoreConfig(mainConf, trackConfig) {
             storeClass === 'JBrowse/Store/SeqFeature/TwoBit' ||
             storeClass === 'JBrowse/Store/Sequence/TwoBit' ||
             trackConfig.useAsRefSeqStore) &&
-            !(mainConf.stores && mainConf.stores.refseqs)
+            !((_a = mainConf.stores) === null || _a === void 0 ? void 0 : _a.refseqs)
             ? 'refseqs'
             : `store${objectHash(storeConf)}`;
     // record it

package/esm/JBrowse1Connection/jb1ToJb2.js

@@ -2,6 +2,7 @@ import { openLocation } from '@jbrowse/core/util/io';
 import { objectHash } from '@jbrowse/core/util';
 import { generateUnknownTrackConf, generateUnsupportedTrackConf, guessAdapter, guessTrackType, UNKNOWN, UNSUPPORTED, } from '@jbrowse/core/util/tracks';
 export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
+    var _a;
     const jb2TrackConfig = {
         trackId: objectHash(jb1TrackConfig),
         name: jb1TrackConfig.key || jb1TrackConfig.label,
@@ -11,8 +12,7 @@ export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
     if (description) {
         jb2TrackConfig.description = description;
     }
-    const category = jb1TrackConfig.category ||
-        (jb1TrackConfig.metadata && jb1TrackConfig.metadata.category);
+    const category = jb1TrackConfig.category || ((_a = jb1TrackConfig.metadata) === null || _a === void 0 ? void 0 : _a.category);
     jb2TrackConfig.category = category ? category.split(/\s*\/\s*/) : [];
     const { storeClass } = jb1TrackConfig;
     if (!jb1TrackConfig.urlTemplate) {

package/esm/JBrowse1Connection/model.js

@@ -12,7 +12,7 @@ export default function (pluginManager) {
     }))
         .actions(self => ({
         async connect() {
-            var _a;
+            var _a, _b;
             const session = getSession(self);
             try {
                 const dataDirLocation = getConf(self, 'dataDirLocation');
@@ -23,14 +23,11 @@ export default function (pluginManager) {
                 if (!assemblyName) {
                     throw new Error('assembly name required for JBrowse 1 connection');
                 }
-                const assemblyConf = session.assemblies.find(a => readConfObject(a, 'name') === assemblyName);
-                if (!assemblyConf) {
+                const conf = session.assemblies.find(a => readConfObject(a, 'name') === assemblyName);
+                if (!conf) {
                     throw new Error(`Assembly "${assemblyName}" not found`);
                 }
-                const sequenceAdapter = readConfObject(assemblyConf, [
-                    'sequence',
-                    'adapter',
-                ]);
+                const sequenceAdapter = readConfObject(conf, ['sequence', 'adapter']);
                 // @ts-expect-error
                 const jb2Tracks = (_a = config.tracks) === null || _a === void 0 ? void 0 : _a.map(jb1Track => ({
                     ...convertTrackConfig(jb1Track, config.dataRoot || '', sequenceAdapter),
@@ -41,7 +38,7 @@ export default function (pluginManager) {
             catch (error) {
                 console.error(error);
                 session.notify(`There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`, 'error');
-                session.breakConnection(self.configuration);
+                (_b = session.breakConnection) === null || _b === void 0 ? void 0 : _b.call(session, self.configuration);
             }
         },
     }));

package/esm/JBrowse1Connection/util.js

@@ -1,11 +1,11 @@
 import getValue from 'get-value';
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 export function isTrack(arg) {
-    return arg && arg.label && typeof arg.label === 'string';
+    return (arg === null || arg === void 0 ? void 0 : arg.label) && typeof arg.label === 'string';
 }
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 export function isSource(arg) {
-    return arg && arg.url && typeof arg.url === 'string';
+    return (arg === null || arg === void 0 ? void 0 : arg.url) && typeof arg.url === 'string';
 }
 export function deepUpdate(a, b) {
     for (const prop of Object.keys(b)) {

package/esm/JBrowse1TextSearchAdapter/HttpMap.js

@@ -6,7 +6,7 @@ import crc32 from 'buffer-crc32';
 export default class HttpMap {
     constructor(args) {
         // make sure url has a trailing slash
-        this.url = /\/$/.test(args.url) ? args.url : `${args.url}/`;
+        this.url = args.url.endsWith('/') ? args.url : `${args.url}/`;
     }
     /**
      * loads meta.json file from names directory and reads number of hash_bits used

package/esm/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.d.ts

@@ -14,7 +14,7 @@ interface SearchResults {
     } | string)[];
     exact: [string, number, string, string, number, number][];
 }
-export type NamesIndexRecord = string | Array<string | number>;
+export type NamesIndexRecord = string | (string | number)[];
 type IndexFile = Record<string, SearchResults>;
 export default class JBrowse1TextSearchAdapter extends BaseAdapter implements BaseTextSearchAdapter {
     httpMap: HttpMap;

package/esm/NCListAdapter/NCListAdapter.js

@@ -41,8 +41,9 @@ export default class NCListAdapter extends BaseFeatureDataAdapter {
         return new NCListFeature(ncFeature, undefined, `${this.id}-${ncFeature.id()}`);
     }
     async hasDataForRefName(refName) {
+        var _a;
         const root = await this.nclist.getDataRoot(refName);
-        return !!(root && root.stats && root.stats.featureCount);
+        return !!((_a = root === null || root === void 0 ? void 0 : root.stats) === null || _a === void 0 ? void 0 : _a.featureCount);
     }
     /**
      * NCList is unable to get list of ref names so returns empty

package/esm/NCListAdapter/NCListFeature.js

@@ -4,8 +4,9 @@ const jb1ToJb2 = { seq_id: 'refName' };
  * wrapper to adapt nclist features to act like jbrowse 2 features
  */
 export default class NCListFeature {
+    constructor(
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    constructor(ncFeature, parent, id) {
+    ncFeature, parent, id) {
         this.ncFeature = ncFeature;
         this.uniqueId = id || ncFeature.id();
         this.parentHandle = parent;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "2.6.2",
+  "version": "2.7.0",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
     "jbrowse",
@@ -45,7 +45,7 @@
   "peerDependencies": {
     "@jbrowse/core": "^2.0.0",
     "mobx": "^6.0.0",
-    "mobx-react": "^7.0.0",
+    "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
     "rxjs": "^7.0.0"
   },
@@ -55,5 +55,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
+  "gitHead": "dbe7fb1af01fc89f833d2744635eb44a17365b41"
 }