@jbrowse/plugin-legacy-jbrowse 2.1.0 → 2.1.3

package/dist/JBrowse1Connection/jb1ToJb2.js

@@ -1,87 +1,40 @@
 "use strict";
-var __assign = (this && this.__assign) || function () {
-    __assign = Object.assign || function(t) {
-        for (var s, i = 1, n = arguments.length; i < n; i++) {
-            s = arguments[i];
-            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
-                t[p] = s[p];
-        }
-        return t;
-    };
-    return __assign.apply(this, arguments);
-};
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
-var __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (_) try {
-            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.createRefSeqsAdapter = exports.convertTrackConfig = void 0;
-var io_1 = require("@jbrowse/core/util/io");
-var util_1 = require("@jbrowse/core/util");
-var tracks_1 = require("@jbrowse/core/util/tracks");
+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 jb2TrackConfig = {
+    const jb2TrackConfig = {
         trackId: (0, util_1.objectHash)(jb1TrackConfig),
         name: jb1TrackConfig.key || jb1TrackConfig.label,
     };
-    var description = jb1TrackConfig.metadata &&
+    const description = jb1TrackConfig.metadata &&
         (jb1TrackConfig.metadata.description || jb1TrackConfig.metadata.Description);
     if (description) {
         jb2TrackConfig.description = description;
     }
-    var category = jb1TrackConfig.category ||
+    const category = jb1TrackConfig.category ||
         (jb1TrackConfig.metadata && jb1TrackConfig.metadata.category);
     jb2TrackConfig.category = category ? category.split(/\s*\/\s*/) : [];
-    var storeClass = jb1TrackConfig.storeClass;
+    const { storeClass } = jb1TrackConfig;
     if (!jb1TrackConfig.urlTemplate) {
         if (!(storeClass && storeClass.endsWith('FromConfig'))) {
-            var trackIdentifier = jb1TrackConfig.key || jb1TrackConfig.label;
-            console.warn("Could not import JBrowse1 track \"".concat(trackIdentifier, "\" because it does not have a \"urlTemplate\" or is not a \"FromConfig\" track"));
+            const trackIdentifier = jb1TrackConfig.key || jb1TrackConfig.label;
+            console.warn(`Could not import JBrowse1 track "${trackIdentifier}" because it does not have a "urlTemplate" or is not a "FromConfig" track`);
             return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, trackIdentifier, jb2TrackConfig.category);
         }
         return generateFromConfigTrackConfig(jb1TrackConfig, jb2TrackConfig);
     }
-    var resolveUrlTemplate = function (urlTemplate) {
-        return new URL(urlTemplate, "".concat(dataRoot, "/")).href
+    const resolveUrlTemplate = (urlTemplate) => {
+        return new URL(urlTemplate, `${dataRoot}/`).href
             .replace(/%7B/gi, '{')
             .replace(/%7D/gi, '}');
     };
-    var urlTemplate = resolveUrlTemplate(jb1TrackConfig.urlTemplate);
+    const urlTemplate = resolveUrlTemplate(jb1TrackConfig.urlTemplate);
     if (storeClass) {
         if (storeClass === 'JBrowse/Store/SeqFeature/BAM') {
-            var adapter = {
+            const adapter = {
                 type: 'BamAdapter',
                 bamLocation: { uri: urlTemplate, locationType: 'UriLocation' },
             };
@@ -104,16 +57,20 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
             }
             else {
                 adapter.index = {
-                    location: { uri: "".concat(urlTemplate, ".bai"), locationType: 'UriLocation' },
+                    location: { uri: `${urlTemplate}.bai`, locationType: 'UriLocation' },
                 };
             }
-            return __assign(__assign({}, jb2TrackConfig), { type: 'AlignmentsTrack', adapter: adapter });
+            return {
+                ...jb2TrackConfig,
+                type: 'AlignmentsTrack',
+                adapter,
+            };
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/CRAM') {
-            var adapter = {
+            const adapter = {
                 type: 'CramAdapter',
                 cramLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                sequenceAdapter: sequenceAdapter,
+                sequenceAdapter,
             };
             if (jb1TrackConfig.craiUrlTemplate) {
                 adapter.craiLocation = {
@@ -123,17 +80,25 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
             }
             else {
                 adapter.craiLocation = {
-                    uri: "".concat(urlTemplate, ".crai"),
+                    uri: `${urlTemplate}.crai`,
                     locationType: 'UriLocation',
                 };
             }
-            return __assign(__assign({}, jb2TrackConfig), { type: 'AlignmentsTrack', adapter: adapter });
+            return {
+                ...jb2TrackConfig,
+                type: 'AlignmentsTrack',
+                adapter,
+            };
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/NCList') {
-            return __assign(__assign({}, jb2TrackConfig), { type: 'FeatureTrack', adapter: {
+            return {
+                ...jb2TrackConfig,
+                type: 'FeatureTrack',
+                adapter: {
                     type: 'NCListAdapter',
                     rootUrlTemplate: { uri: urlTemplate, locationType: 'UriLocation' },
-                } });
+                },
+            };
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/BigWig' ||
             storeClass === 'JBrowse/Store/BigWig') {
@@ -144,13 +109,17 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
                 jb1TrackConfig.type.endsWith('Density')) {
                 jb2TrackConfig.defaultRendering = 'density';
             }
-            return __assign(__assign({}, jb2TrackConfig), { type: 'QuantitativeTrack', adapter: {
+            return {
+                ...jb2TrackConfig,
+                type: 'QuantitativeTrack',
+                adapter: {
                     type: 'BigWigAdapter',
                     bigWigLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                } });
+                },
+            };
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/VCFTabix') {
-            var adapter = {
+            const adapter = {
                 type: 'VcfTabixAdapter',
                 vcfGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },
             };
@@ -173,28 +142,40 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
             }
             else {
                 adapter.index = {
-                    location: { uri: "".concat(urlTemplate, ".tbi"), locationType: 'UriLocation' },
+                    location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },
                 };
             }
-            return __assign(__assign({}, jb2TrackConfig), { type: 'VariantTrack', adapter: adapter });
+            return {
+                ...jb2TrackConfig,
+                type: 'VariantTrack',
+                adapter,
+            };
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/VCFTribble') {
-            return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, "VCFTribble (".concat(urlTemplate, ")"), jb2TrackConfig.category);
+            return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, `VCFTribble (${urlTemplate})`, jb2TrackConfig.category);
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/GFF3') {
-            return __assign(__assign({}, jb2TrackConfig), { type: 'FeatureTrack', adapter: {
+            return {
+                ...jb2TrackConfig,
+                type: 'FeatureTrack',
+                adapter: {
                     type: 'Gff3Adapter',
                     gffLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                } });
+                },
+            };
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/BigBed') {
-            return __assign(__assign({}, jb2TrackConfig), { type: 'FeatureTrack', adapter: {
+            return {
+                ...jb2TrackConfig,
+                type: 'FeatureTrack',
+                adapter: {
                     type: 'BigBedAdapter',
                     bigBedLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                } });
+                },
+            };
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/GFF3Tabix') {
-            var adapter = {
+            const adapter = {
                 type: 'Gff3TabixAdapter',
                 gffGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },
             };
@@ -217,16 +198,20 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
             }
             else {
                 adapter.index = {
-                    location: { uri: "".concat(urlTemplate, ".tbi"), locationType: 'UriLocation' },
+                    location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },
                 };
             }
-            return __assign(__assign({}, jb2TrackConfig), { type: 'FeatureTrack', adapter: adapter });
+            return {
+                ...jb2TrackConfig,
+                type: 'FeatureTrack',
+                adapter,
+            };
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/BED') {
-            return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, "BED (".concat(urlTemplate, ")"), jb2TrackConfig.category);
+            return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, `BED (${urlTemplate})`, jb2TrackConfig.category);
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/BEDTabix') {
-            var adapter = {
+            const adapter = {
                 type: 'BedTabixAdapter',
                 bedGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },
             };
@@ -249,26 +234,34 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
             }
             else {
                 adapter.index = {
-                    location: { uri: "".concat(urlTemplate, ".tbi"), locationType: 'UriLocation' },
+                    location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },
                 };
             }
-            return __assign(__assign({}, jb2TrackConfig), { type: 'FeatureTrack', adapter: adapter });
+            return {
+                ...jb2TrackConfig,
+                type: 'FeatureTrack',
+                adapter,
+            };
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/GTF') {
-            return __assign(__assign({}, jb2TrackConfig), { type: 'FeatureTrack', adapter: {
+            return {
+                ...jb2TrackConfig,
+                type: 'FeatureTrack',
+                adapter: {
                     type: 'GtfAdapter',
                     gtfLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                } });
+                },
+            };
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/StaticChunked' ||
             storeClass === 'JBrowse/Store/Sequence/StaticChunked') {
-            return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, "StaticChunked (".concat(urlTemplate, ")"), jb2TrackConfig.category);
+            return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, `StaticChunked (${urlTemplate})`, jb2TrackConfig.category);
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/UnindexedFasta') {
-            return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, "UnindexedFasta (".concat(urlTemplate, ")"), jb2TrackConfig.category);
+            return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, `UnindexedFasta (${urlTemplate})`, jb2TrackConfig.category);
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/IndexedFasta') {
-            var adapter = {
+            const adapter = {
                 type: 'IndexedFastaAdapter',
                 fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },
             };
@@ -280,14 +273,18 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
             }
             else {
                 adapter.faiLocation = {
-                    uri: "".concat(urlTemplate, ".fai"),
+                    uri: `${urlTemplate}.fai`,
                     locationType: 'UriLocation',
                 };
             }
-            return __assign(__assign({}, jb2TrackConfig), { type: 'SequenceTrack', adapter: adapter });
+            return {
+                ...jb2TrackConfig,
+                type: 'SequenceTrack',
+                adapter,
+            };
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/BgzipIndexedFasta') {
-            var adapter = {
+            const adapter = {
                 type: 'BgzipFastaAdapter',
                 fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },
             };
@@ -299,7 +296,7 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
             }
             else {
                 adapter.faiLocation = {
-                    uri: "".concat(urlTemplate, ".fai"),
+                    uri: `${urlTemplate}.fai`,
                     locationType: 'UriLocation',
                 };
             }
@@ -311,17 +308,25 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
             }
             else {
                 adapter.gziLocation = {
-                    uri: "".concat(urlTemplate, ".gzi"),
+                    uri: `${urlTemplate}.gzi`,
                     locationType: 'UriLocation',
                 };
             }
-            return __assign(__assign({}, jb2TrackConfig), { type: 'ReferenceSequenceTrack', adapter: adapter });
+            return {
+                ...jb2TrackConfig,
+                type: 'ReferenceSequenceTrack',
+                adapter,
+            };
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/TwoBit') {
-            return __assign(__assign({}, jb2TrackConfig), { type: 'ReferenceSequenceTrack', adapter: {
+            return {
+                ...jb2TrackConfig,
+                type: 'ReferenceSequenceTrack',
+                adapter: {
                     type: 'TwoBitAdapter',
                     twoBitLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                } });
+                },
+            };
         }
     }
     // If we don't recogize the store class, make a best effort to guess by file type
@@ -348,11 +353,11 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
 }
 exports.convertTrackConfig = convertTrackConfig;
 function generateFromConfigTrackConfig(jb1TrackConfig, jb2TrackConfig) {
-    var jb1Features = jb1TrackConfig.features || [];
-    var jb2Features = jb1Features.map(function (feature) {
-        var jb2Feature = JSON.parse(JSON.stringify(feature));
+    const jb1Features = jb1TrackConfig.features || [];
+    const jb2Features = jb1Features.map((feature) => {
+        const jb2Feature = JSON.parse(JSON.stringify(feature));
         jb2Feature.refName = feature.seq_id;
-        jb2Feature.uniqueId = "".concat(feature.seq_id, ":").concat(feature.start, "-").concat(feature.end, ":").concat(feature.name || '');
+        jb2Feature.uniqueId = `${feature.seq_id}:${feature.start}-${feature.end}:${feature.name || ''}`;
         return jb2Feature;
     });
     jb2TrackConfig.adapter = {
@@ -362,72 +367,63 @@ function generateFromConfigTrackConfig(jb1TrackConfig, jb2TrackConfig) {
     jb2TrackConfig.type = 'FeatureTrack';
     return jb2TrackConfig;
 }
-function createRefSeqsAdapter(refSeqs) {
-    return __awaiter(this, void 0, void 0, function () {
-        var refSeqsJson, refSeqsData;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    if (typeof refSeqs === 'string') {
-                        // assume refSeqs is a url if it is string
-                        refSeqs = {
-                            url: refSeqs,
-                        };
-                    }
-                    if (!refSeqs.url) return [3 /*break*/, 2];
-                    if (refSeqs.url.match(/.fai$/)) {
-                        return [2 /*return*/, {
-                                type: 'IndexedFastaAdapter',
-                                fastaLocation: {
-                                    uri: refSeqs.url.slice(0, -4),
-                                    locationType: 'UriLocation',
-                                },
-                                faiLocation: {
-                                    uri: refSeqs.url,
-                                    locationType: 'UriLocation',
-                                },
-                            }];
-                    }
-                    if (refSeqs.url.match(/.2bit$/)) {
-                        return [2 /*return*/, {
-                                type: 'TwoBitAdapter',
-                                twoBitLocation: { uri: refSeqs.url, locationType: 'UriLocation' },
-                            }];
-                    }
-                    if (refSeqs.url.match(/.fa$/)) {
-                        throw new Error('Unindexed FASTA adapter not available');
-                    }
-                    if (refSeqs.url.match(/.sizes/)) {
-                        throw new Error('chromosome SIZES adapter not available');
-                    }
-                    return [4 /*yield*/, (0, io_1.openLocation)({
-                            uri: refSeqs.url,
-                            locationType: 'UriLocation',
-                        }).readFile('utf8')];
-                case 1:
-                    refSeqsJson = _a.sent();
-                    refSeqsData = JSON.parse(refSeqsJson);
-                    return [2 /*return*/, refSeqAdapterFromConfig(refSeqsData)];
-                case 2:
-                    if ('data' in refSeqs) {
-                        return [2 /*return*/, refSeqAdapterFromConfig(refSeqs.data || [])];
-                    }
-                    throw new Error("Could not determine adapter for JBrowse1 refSeqs: ".concat(refSeqs.url || JSON.stringify(refSeqs)));
-            }
-        });
-    });
+async function createRefSeqsAdapter(refSeqs) {
+    if (typeof refSeqs === 'string') {
+        // assume refSeqs is a url if it is string
+        refSeqs = {
+            url: refSeqs,
+        };
+    }
+    // check refseq urls
+    if (refSeqs.url) {
+        if (refSeqs.url.match(/.fai$/)) {
+            return {
+                type: 'IndexedFastaAdapter',
+                fastaLocation: {
+                    uri: refSeqs.url.slice(0, -4),
+                    locationType: 'UriLocation',
+                },
+                faiLocation: {
+                    uri: refSeqs.url,
+                    locationType: 'UriLocation',
+                },
+            };
+        }
+        if (refSeqs.url.match(/.2bit$/)) {
+            return {
+                type: 'TwoBitAdapter',
+                twoBitLocation: { uri: refSeqs.url, locationType: 'UriLocation' },
+            };
+        }
+        if (refSeqs.url.match(/.fa$/)) {
+            throw new Error('Unindexed FASTA adapter not available');
+        }
+        if (refSeqs.url.match(/.sizes/)) {
+            throw new Error('chromosome SIZES adapter not available');
+        }
+        const refSeqsJson = await (0, io_1.openLocation)({
+            uri: refSeqs.url,
+            locationType: 'UriLocation',
+        }).readFile('utf8');
+        const refSeqsData = JSON.parse(refSeqsJson);
+        return refSeqAdapterFromConfig(refSeqsData);
+    }
+    if ('data' in refSeqs) {
+        return refSeqAdapterFromConfig(refSeqs.data || []);
+    }
+    throw new Error(`Could not determine adapter for JBrowse1 refSeqs: ${refSeqs.url || JSON.stringify(refSeqs)}`);
 }
 exports.createRefSeqsAdapter = createRefSeqsAdapter;
 function refSeqAdapterFromConfig(refSeqsData) {
-    var features = refSeqsData.map(function (refSeq) { return ({
+    const features = refSeqsData.map((refSeq) => ({
         refName: refSeq.name,
         uniqueId: refSeq.name,
         start: refSeq.start,
         end: refSeq.end,
-    }); });
+    }));
     return {
         type: 'FromConfigAdapter',
-        features: features,
+        features,
     };
 }
 //# sourceMappingURL=jb1ToJb2.js.map

package/dist/JBrowse1Connection/jb1ToJb2.js.map

@@ -1 +1 @@
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package/dist/JBrowse1Connection/model.js

@@ -3,48 +3,48 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var configuration_1 = require("@jbrowse/core/configuration");
-var util_1 = require("@jbrowse/core/util");
-var models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-var mobx_state_tree_1 = require("mobx-state-tree");
-var configSchema_1 = __importDefault(require("./configSchema"));
-var jb1ConfigLoad_1 = require("./jb1ConfigLoad");
-var jb1ToJb2_1 = require("./jb1ToJb2");
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const configSchema_1 = __importDefault(require("./configSchema"));
+const jb1ConfigLoad_1 = require("./jb1ConfigLoad");
+const jb1ToJb2_1 = require("./jb1ToJb2");
 function default_1(pluginManager) {
     return mobx_state_tree_1.types.compose('JBrowse1Connection', (0, models_1.BaseConnectionModelFactory)(pluginManager), mobx_state_tree_1.types
         .model({
         configuration: (0, configuration_1.ConfigurationReference)(configSchema_1.default),
         type: mobx_state_tree_1.types.literal('JBrowse1Connection'),
     })
-        .actions(function (self) { return ({
-        connect: function () {
-            var dataDirLocation = (0, configuration_1.readConfObject)(self.configuration, 'dataDirLocation');
-            var session = (0, util_1.getSession)(self);
+        .actions(self => ({
+        connect() {
+            const dataDirLocation = (0, configuration_1.readConfObject)(self.configuration, 'dataDirLocation');
+            const session = (0, util_1.getSession)(self);
             (0, jb1ConfigLoad_1.fetchJb1)(dataDirLocation)
-                .then(function (config) {
-                var assemblyName = (0, configuration_1.readConfObject)(self.configuration, 'assemblyNames')[0];
+                .then(config => {
+                const assemblyName = (0, configuration_1.readConfObject)(self.configuration, 'assemblyNames')[0];
                 if (!assemblyName) {
                     throw new Error('assembly name required for JBrowse 1 connection');
                 }
-                var assemblyConf = session.assemblies.find(function (assembly) { return (0, configuration_1.readConfObject)(assembly, 'name') === assemblyName; });
-                var sequenceAdapter = (0, configuration_1.readConfObject)(assemblyConf, [
+                const assemblyConf = session.assemblies.find(assembly => (0, configuration_1.readConfObject)(assembly, 'name') === assemblyName);
+                const sequenceAdapter = (0, configuration_1.readConfObject)(assemblyConf, [
                     'sequence',
                     'adapter',
                 ]);
-                var jb2Tracks = config.tracks.map(function (jb1Track) {
-                    var jb2Track = (0, jb1ToJb2_1.convertTrackConfig)(jb1Track, config.dataRoot, sequenceAdapter);
+                const jb2Tracks = config.tracks.map(jb1Track => {
+                    const jb2Track = (0, jb1ToJb2_1.convertTrackConfig)(jb1Track, config.dataRoot, sequenceAdapter);
                     jb2Track.assemblyNames = [assemblyName];
                     return jb2Track;
                 });
                 self.setTrackConfs(jb2Tracks);
             })
-                .catch(function (error) {
+                .catch(error => {
                 console.error(error);
-                session.notify("There was a problem connecting to the JBrowse 1 data directory \"".concat(self.name, "\". Please make sure you have entered a valid location. The error that was thrown is: \"").concat(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);
             });
         },
-    }); }));
+    })));
 }
 exports.default = default_1;
 //# sourceMappingURL=model.js.map

package/dist/JBrowse1Connection/model.js.map

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+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/model.js"],"names":[],"mappings":";;;;;AAAA,+DAGoC;AACpC,6CAA+C;AAC/C,uEAAuF;AACvF,qDAAuC;AACvC,kEAAyC;AAEzC,mDAA0C;AAC1C,yCAA+C;AAE/C,mBAAyB,aAAa;IACpC,OAAO,uBAAK,CAAC,OAAO,CAClB,oBAAoB,EACpB,IAAA,mCAA0B,EAAC,aAAa,CAAC,EACzC,uBAAK;SACF,KAAK,CAAC;QACL,aAAa,EAAE,IAAA,sCAAsB,EAAC,sBAAY,CAAC;QACnD,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,oBAAoB,CAAC;KAC1C,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,OAAO;YACL,MAAM,eAAe,GAAG,IAAA,8BAAc,EACpC,IAAI,CAAC,aAAa,EAClB,iBAAiB,CAClB,CAAA;YACD,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;YAChC,IAAA,wBAAQ,EAAC,eAAe,CAAC;iBACtB,IAAI,CAAC,MAAM,CAAC,EAAE;gBACb,MAAM,YAAY,GAAG,IAAA,8BAAc,EACjC,IAAI,CAAC,aAAa,EAClB,eAAe,CAChB,CAAC,CAAC,CAAC,CAAA;gBACJ,IAAI,CAAC,YAAY,EAAE;oBACjB,MAAM,IAAI,KAAK,CACb,iDAAiD,CAClD,CAAA;iBACF;gBACD,MAAM,YAAY,GAAG,OAAO,CAAC,UAAU,CAAC,IAAI,CAC1C,QAAQ,CAAC,EAAE,CAAC,IAAA,8BAAc,EAAC,QAAQ,EAAE,MAAM,CAAC,KAAK,YAAY,CAC9D,CAAA;gBACD,MAAM,eAAe,GAAG,IAAA,8BAAc,EAAC,YAAY,EAAE;oBACnD,UAAU;oBACV,SAAS;iBACV,CAAC,CAAA;gBACF,MAAM,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE;oBAC7C,MAAM,QAAQ,GAAG,IAAA,6BAAkB,EACjC,QAAQ,EACR,MAAM,CAAC,QAAQ,EACf,eAAe,CAChB,CAAA;oBACD,QAAQ,CAAC,aAAa,GAAG,CAAC,YAAY,CAAC,CAAA;oBACvC,OAAO,QAAQ,CAAA;gBACjB,CAAC,CAAC,CAAA;gBACF,IAAI,CAAC,aAAa,CAAC,SAAS,CAAC,CAAA;YAC/B,CAAC,CAAC;iBACD,KAAK,CAAC,KAAK,CAAC,EAAE;gBACb,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;gBACpB,OAAO,CAAC,MAAM,CACZ,mEAAmE,IAAI,CAAC,IAAI,yFAAyF,KAAK,GAAG,EAC7K,OAAO,CACR,CAAA;gBACD,OAAO,CAAC,eAAe,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;YAC7C,CAAC,CAAC,CAAA;QACN,CAAC;KACF,CAAC,CAAC,CACN,CAAA;AACH,CAAC;AAxDD,4BAwDC"}