@jbrowse/plugin-legacy-jbrowse 2.1.0 → 2.1.3

package/dist/JBrowse1Connection/jb1ConfigParse.js

@@ -1,69 +1,22 @@
 "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 __read = (this && this.__read) || function (o, n) {
-    var m = typeof Symbol === "function" && o[Symbol.iterator];
-    if (!m) return o;
-    var i = m.call(o), r, ar = [], e;
-    try {
-        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
-    }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    return ar;
-};
-var __values = (this && this.__values) || function(o) {
-    var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
-    if (m) return m.call(o);
-    if (o && typeof o.length === "number") return {
-        next: function () {
-            if (o && i >= o.length) o = void 0;
-            return { value: o && o[i++], done: !o };
-        }
-    };
-    throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
-};
-var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
-    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
-        if (ar || !(i in from)) {
-            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
-            ar[i] = from[i];
-        }
-    }
-    return to.concat(ar || Array.prototype.slice.call(from));
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.regularizeConf = exports.parseJB1Conf = exports.parseJB1Json = void 0;
 /* eslint no-cond-assign: ["error", "except-parens"] */
-var get_value_1 = __importDefault(require("get-value"));
-var set_value_1 = __importDefault(require("set-value"));
-var util_1 = require("@jbrowse/core/util");
-var util_2 = require("./util");
+const get_value_1 = __importDefault(require("get-value"));
+const set_value_1 = __importDefault(require("set-value"));
+const util_1 = require("@jbrowse/core/util");
+const util_2 = require("./util");
 function parseJB1Json(config, url) {
     if (typeof config === 'string') {
-        var parsedConf = void 0;
+        let parsedConf;
         try {
             parsedConf = JSON.parse(config);
         }
         catch (error) {
-            throw new Error("".concat(error, " when parsing configuration."));
+            throw new Error(`${error} when parsing configuration.`);
         }
         return regularizeConf(parsedConf, url);
     }
@@ -71,12 +24,12 @@ function parseJB1Json(config, url) {
 }
 exports.parseJB1Json = parseJB1Json;
 function parseJB1Conf(config, url) {
-    var parsedConf;
+    let parsedConf;
     try {
         parsedConf = parse(config, url);
     }
     catch (error) {
-        throw new Error("".concat(error, " when parsing configuration."));
+        throw new Error(`${error} when parsing configuration.`);
     }
     return regularizeConf(parsedConf, url);
 }
@@ -88,18 +41,18 @@ function isAlwaysArray(varName) {
     return false;
 }
 function parse(text, url) {
-    var section = [];
-    var keyPath;
-    var operation;
-    var value;
-    var data = { tracks: {} };
-    var lineNumber;
+    let section = [];
+    let keyPath;
+    let operation;
+    let value;
+    const data = { tracks: {} };
+    let lineNumber;
     function recordVal() {
         if (value !== undefined) {
-            var parsedValue = void 0;
+            let parsedValue;
             try {
                 // parse json
-                var match = value.match(/^json:(.+)/i);
+                const match = value.match(/^json:(.+)/i);
                 if (match) {
                     parsedValue = JSON.parse(match[1]);
                 }
@@ -111,11 +64,11 @@ function parse(text, url) {
                     parsedValue = value;
                 }
                 if (!keyPath) {
-                    throw new Error("Error parsing in section ".concat(section.join(' - ')));
+                    throw new Error(`Error parsing in section ${section.join(' - ')}`);
                 }
-                var path = section.concat(keyPath).join('.');
+                const path = section.concat(keyPath).join('.');
                 if (operation === '+=') {
-                    var existing = (0, get_value_1.default)(data, path);
+                    let existing = (0, get_value_1.default)(data, path);
                     if (existing) {
                         if (!Array.isArray(existing)) {
                             existing = [existing];
@@ -136,16 +89,15 @@ function parse(text, url) {
                 (0, set_value_1.default)(data, path, parsedValue);
             }
             catch (e) {
-                throw new Error("syntax error".concat(url ? " in ".concat(url) : '').concat(lineNumber ? " at line ".concat(lineNumber - 1) : ''));
+                throw new Error(`syntax error${url ? ` in ${url}` : ''}${lineNumber ? ` at line ${lineNumber - 1}` : ''}`);
             }
         }
     }
-    text.split('\n').forEach(function (textLine, i) {
-        var _a;
+    text.split('\n').forEach((textLine, i) => {
         lineNumber = i + 1;
-        var line = textLine.replace(/^\s*#.+/, '');
+        const line = textLine.replace(/^\s*#.+/, '');
         // new section
-        var match;
+        let match;
         if ((match = line.match(/^\s*\[([^\]]+)/))) {
             // new section
             recordVal();
@@ -160,7 +112,7 @@ function parse(text, url) {
         else if ((match = line.match(value === undefined ? /^([^+=]+)(\+?=)(.*)/ : /^(\S[^+=]+)(\+?=)(.*)/))) {
             recordVal();
             keyPath = match[1].trim().split(/\s*\.\s*/);
-            _a = __read(match, 3), operation = _a[2];
+            [, , operation] = match;
             if (isAlwaysArray(section.concat(keyPath).join('.'))) {
                 operation = '+=';
             }
@@ -175,7 +127,7 @@ function parse(text, url) {
         }
         // add to existing value
         else if (value !== undefined && (match = line.match(/^\s+(\S.*)/))) {
-            value += value.length ? " ".concat(match[1].trim()) : match[1].trim();
+            value += value.length ? ` ${match[1].trim()}` : match[1].trim();
         }
         // done with last value
         else {
@@ -195,7 +147,6 @@ function parse(text, url) {
  * @returns the same object it was passed
  */
 function regularizeConf(conf, url) {
-    var e_1, _a, e_2, _b;
     // if tracks is not an array, convert it to one
     if (conf.tracks && !Array.isArray(conf.tracks)) {
         // if it's a single track config, wrap it in an arrayref
@@ -204,31 +155,21 @@ function regularizeConf(conf, url) {
         }
         // otherwise, coerce it to an array
         else {
-            var tracks = [];
-            try {
-                for (var _c = __values(Object.keys(conf.tracks)), _d = _c.next(); !_d.done; _d = _c.next()) {
-                    var label = _d.value;
-                    var track = conf.tracks[label];
-                    if ((0, util_2.isTrack)(track)) {
-                        tracks.push(track);
-                    }
-                    else {
-                        tracks.push(__assign({ label: label }, track));
-                    }
+            const tracks = [];
+            for (const label of Object.keys(conf.tracks)) {
+                const track = conf.tracks[label];
+                if ((0, util_2.isTrack)(track)) {
+                    tracks.push(track);
                 }
-            }
-            catch (e_1_1) { e_1 = { error: e_1_1 }; }
-            finally {
-                try {
-                    if (_d && !_d.done && (_a = _c.return)) _a.call(_c);
+                else {
+                    tracks.push({ label, ...track });
                 }
-                finally { if (e_1) throw e_1.error; }
             }
             conf.tracks = tracks;
         }
     }
     // regularize trackMetadata.sources
-    var meta = conf.trackMetadata;
+    const meta = conf.trackMetadata;
     if (meta && meta.sources) {
         // if it's a single source config, wrap it in an arrayref
         if (typeof meta.sources === 'string') {
@@ -238,31 +179,21 @@ function regularizeConf(conf, url) {
             meta.sources = [meta.sources];
         }
         if (!Array.isArray(meta.sources)) {
-            var sources = [];
-            try {
-                for (var _e = __values(Object.keys(meta.sources)), _f = _e.next(); !_f.done; _f = _e.next()) {
-                    var name_1 = _f.value;
-                    var source = meta.sources[name_1];
-                    if (!('name' in source)) {
-                        source.name = name_1;
-                    }
-                    sources.push(source);
-                }
-            }
-            catch (e_2_1) { e_2 = { error: e_2_1 }; }
-            finally {
-                try {
-                    if (_f && !_f.done && (_b = _e.return)) _b.call(_e);
+            const sources = [];
+            for (const name of Object.keys(meta.sources)) {
+                const source = meta.sources[name];
+                if (!('name' in source)) {
+                    source.name = name;
                 }
-                finally { if (e_2) throw e_2.error; }
+                sources.push(source);
             }
             meta.sources = sources;
         }
         // coerce any string source defs to be URLs, and try to detect their types
-        meta.sources = meta.sources.map(function (sourceDef) {
+        meta.sources = meta.sources.map((sourceDef) => {
             if (typeof sourceDef === 'string') {
-                var newSourceDef = { url: sourceDef };
-                var typeMatch = sourceDef.match(/\.(\w+)$/);
+                const newSourceDef = { url: sourceDef };
+                const typeMatch = sourceDef.match(/\.(\w+)$/);
                 if (typeMatch) {
                     newSourceDef.type = typeMatch[1].toLowerCase();
                 }
@@ -282,17 +213,17 @@ function regularizeConf(conf, url) {
     if (conf.sourceUrl) {
         // set a default baseUrl in each of the track and store confs, and the names
         // conf, if needed
-        var addBase = [];
+        const addBase = [];
         if (conf.tracks) {
-            addBase.push.apply(addBase, __spreadArray([], __read(conf.tracks), false));
+            addBase.push(...conf.tracks);
         }
         if (conf.stores) {
-            addBase.push.apply(addBase, __spreadArray([], __read(Object.values(conf.stores)), false));
+            addBase.push(...Object.values(conf.stores));
         }
         if (conf.names) {
             addBase.push(conf.names);
         }
-        addBase.forEach(function (t) {
+        addBase.forEach((t) => {
             if (!t.baseUrl) {
                 t.baseUrl = conf.baseUrl || '/';
             }
@@ -306,19 +237,19 @@ function regularizeConf(conf, url) {
         }
     }
     conf.stores = conf.stores || {};
-    (conf.tracks || []).forEach(function (trackConfig) {
+    (conf.tracks || []).forEach((trackConfig) => {
         // if there is a `config` subpart, just copy its keys in to the top-level
         // config
         if (trackConfig.config) {
-            var c = trackConfig.config;
+            const c = trackConfig.config;
             delete trackConfig.config;
-            trackConfig = __assign(__assign({}, c), trackConfig);
+            trackConfig = { ...c, ...trackConfig };
         }
         // skip if it's a new-style track def
         if (trackConfig.store) {
             return;
         }
-        var trackClassName;
+        let trackClassName;
         if (trackConfig.type === 'FeatureTrack') {
             trackClassName = 'JBrowse/View/Track/HTMLFeatures';
         }
@@ -356,7 +287,7 @@ function regularizeClass(root, className) {
         return '';
     }
     if (!className.includes('/')) {
-        className = "".concat(root, "/").concat(className);
+        className = `${root}/${className}`;
     }
     className = className.replace(/^\//, '');
     return className;
@@ -366,10 +297,10 @@ function guessStoreClass(trackConfig, urlTemplate) {
         return '';
     }
     if (trackConfig.type && trackConfig.type.includes('/FixedImage')) {
-        return "JBrowse/Store/TiledImage/Fixed".concat(trackConfig.backendVersion === 0 ? '_v0' : '');
+        return `JBrowse/Store/TiledImage/Fixed${trackConfig.backendVersion === 0 ? '_v0' : ''}`;
     }
     if (/\.jsonz?$/i.test(urlTemplate)) {
-        return "JBrowse/Store/SeqFeature/NCList".concat(trackConfig.backendVersion === 0 ? '_v0' : '');
+        return `JBrowse/Store/SeqFeature/NCList${trackConfig.backendVersion === 0 ? '_v0' : ''}`;
     }
     if (/\.bam$/i.test(urlTemplate)) {
         return 'JBrowse/Store/SeqFeature/BAM';
@@ -415,8 +346,8 @@ function guessStoreClass(trackConfig, urlTemplate) {
 function synthesizeTrackStoreConfig(mainConf, trackConfig) {
     // figure out what data store class to use with the track, applying some
     // defaults if it is not explicit in the configuration
-    var _a = trackConfig.urlTemplate, urlTemplate = _a === void 0 ? '' : _a;
-    var storeClass;
+    const { urlTemplate = '' } = trackConfig;
+    let storeClass;
     if (trackConfig.storeClass) {
         storeClass = regularizeClass('JBrowse/Store', trackConfig.storeClass);
     }
@@ -424,11 +355,11 @@ function synthesizeTrackStoreConfig(mainConf, trackConfig) {
         storeClass = guessStoreClass(trackConfig, urlTemplate);
     }
     if (!storeClass) {
-        console.warn("Unable to determine an appropriate data store to use with track '".concat(trackConfig.label, "', please explicitly specify a storeClass in the configuration."));
+        console.warn(`Unable to determine an appropriate data store to use with track '${trackConfig.label}', please explicitly specify a storeClass in the configuration.`);
         return;
     }
     // synthesize a separate store conf
-    var storeConf = __assign(__assign({}, trackConfig), { type: storeClass });
+    const storeConf = { ...trackConfig, type: storeClass };
     // if this is the first sequence store we see, and we have no refseqs store
     // defined explicitly, make this the refseqs store.
     if ((storeClass === 'JBrowse/Store/Sequence/StaticChunked' ||
@@ -442,7 +373,7 @@ function synthesizeTrackStoreConfig(mainConf, trackConfig) {
         storeConf.name = 'refseqs';
     }
     else {
-        storeConf.name = "store".concat((0, util_1.objectHash)(storeConf));
+        storeConf.name = `store${(0, util_1.objectHash)(storeConf)}`;
     }
     // record it
     if (!mainConf.stores) {

package/dist/JBrowse1Connection/jb1ConfigParse.js.map

@@ -1 +1 @@
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