@jbrowse/plugin-legacy-jbrowse 1.5.0 → 1.5.4

package/dist/plugin-legacy-jbrowse.esm.js

@@ -6,30 +6,74 @@ import { ConfigurationSchema, readConfObject, ConfigurationReference } from '@jb
 import { BaseAdapter, BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 import crc32 from 'buffer-crc32';
+import { generateUnsupportedTrackConf, guessAdapter, UNSUPPORTED, UNKNOWN, generateUnknownTrackConf, guessTrackType, getFileName } from '@jbrowse/core/util/tracks';
 import { objectHash, getSession, checkAbortSignal } from '@jbrowse/core/util';
 import { baseConnectionConfig, BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models';
 import { types } from 'mobx-state-tree';
 import { openLocation } from '@jbrowse/core/util/io';
 import getValue from 'get-value';
 import setValue from 'set-value';
-import { generateUnsupportedTrackConf, guessAdapter, UNSUPPORTED, UNKNOWN, generateUnknownTrackConf, guessTrackType } from '@jbrowse/core/util/tracks';
 import NCListStore from '@gmod/nclist';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { RemoteFile } from 'generic-filehandle';
 
+function _asyncIterator(iterable) {
+  var method,
+      async,
+      sync,
+      retry = 2;
+
+  for ("undefined" != typeof Symbol && (async = Symbol.asyncIterator, sync = Symbol.iterator); retry--;) {
+    if (async && null != (method = iterable[async])) return method.call(iterable);
+    if (sync && null != (method = iterable[sync])) return new AsyncFromSyncIterator(method.call(iterable));
+    async = "@@asyncIterator", sync = "@@iterator";
+  }
+
+  throw new TypeError("Object is not async iterable");
+}
+
+function AsyncFromSyncIterator(s) {
+  function AsyncFromSyncIteratorContinuation(r) {
+    if (Object(r) !== r) return Promise.reject(new TypeError(r + " is not an object."));
+    var done = r.done;
+    return Promise.resolve(r.value).then(function (value) {
+      return {
+        value: value,
+        done: done
+      };
+    });
+  }
+
+  return AsyncFromSyncIterator = function (s) {
+    this.s = s, this.n = s.next;
+  }, AsyncFromSyncIterator.prototype = {
+    s: null,
+    n: null,
+    next: function () {
+      return AsyncFromSyncIteratorContinuation(this.n.apply(this.s, arguments));
+    },
+    return: function (value) {
+      var ret = this.s.return;
+      return void 0 === ret ? Promise.resolve({
+        value: value,
+        done: !0
+      }) : AsyncFromSyncIteratorContinuation(ret.apply(this.s, arguments));
+    },
+    throw: function (value) {
+      var thr = this.s.return;
+      return void 0 === thr ? Promise.reject(value) : AsyncFromSyncIteratorContinuation(thr.apply(this.s, arguments));
+    }
+  }, new AsyncFromSyncIterator(s);
+}
+
 function ownKeys(object, enumerableOnly) {
   var keys = Object.keys(object);
 
   if (Object.getOwnPropertySymbols) {
     var symbols = Object.getOwnPropertySymbols(object);
-
-    if (enumerableOnly) {
-      symbols = symbols.filter(function (sym) {
-        return Object.getOwnPropertyDescriptor(object, sym).enumerable;
-      });
-    }
-
-    keys.push.apply(keys, symbols);
+    enumerableOnly && (symbols = symbols.filter(function (sym) {
+      return Object.getOwnPropertyDescriptor(object, sym).enumerable;
+    })), keys.push.apply(keys, symbols);
   }
 
   return keys;
@@ -37,19 +81,12 @@ function ownKeys(object, enumerableOnly) {
 
 function _objectSpread2(target) {
   for (var i = 1; i < arguments.length; i++) {
-    var source = arguments[i] != null ? arguments[i] : {};
-
-    if (i % 2) {
-      ownKeys(Object(source), true).forEach(function (key) {
-        _defineProperty(target, key, source[key]);
-      });
-    } else if (Object.getOwnPropertyDescriptors) {
-      Object.defineProperties(target, Object.getOwnPropertyDescriptors(source));
-    } else {
-      ownKeys(Object(source)).forEach(function (key) {
-        Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key));
-      });
-    }
+    var source = null != arguments[i] ? arguments[i] : {};
+    i % 2 ? ownKeys(Object(source), !0).forEach(function (key) {
+      _defineProperty(target, key, source[key]);
+    }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) {
+      Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key));
+    });
   }
 
   return target;
@@ -58,31 +95,11 @@ function _objectSpread2(target) {
 function _typeof(obj) {
   "@babel/helpers - typeof";
 
-  if (typeof Symbol === "function" && typeof Symbol.iterator === "symbol") {
-    _typeof = function (obj) {
-      return typeof obj;
-    };
-  } else {
-    _typeof = function (obj) {
-      return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj;
-    };
-  }
-
-  return _typeof(obj);
-}
-
-function _asyncIterator(iterable) {
-  var method;
-
-  if (typeof Symbol !== "undefined") {
-    if (Symbol.asyncIterator) method = iterable[Symbol.asyncIterator];
-    if (method == null && Symbol.iterator) method = iterable[Symbol.iterator];
-  }
-
-  if (method == null) method = iterable["@@asyncIterator"];
-  if (method == null) method = iterable["@@iterator"];
-  if (method == null) throw new TypeError("Object is not async iterable");
-  return method.call(iterable);
+  return _typeof = "function" == typeof Symbol && "symbol" == typeof Symbol.iterator ? function (obj) {
+    return typeof obj;
+  } : function (obj) {
+    return obj && "function" == typeof Symbol && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj;
+  }, _typeof(obj);
 }
 
 function asyncGeneratorStep(gen, resolve, reject, _next, _throw, key, arg) {
@@ -140,6 +157,9 @@ function _defineProperties(target, props) {
 function _createClass(Constructor, protoProps, staticProps) {
   if (protoProps) _defineProperties(Constructor.prototype, protoProps);
   if (staticProps) _defineProperties(Constructor, staticProps);
+  Object.defineProperty(Constructor, "prototype", {
+    writable: false
+  });
   return Constructor;
 }
 
@@ -163,12 +183,15 @@ function _inherits(subClass, superClass) {
     throw new TypeError("Super expression must either be null or a function");
   }
 
-  subClass.prototype = Object.create(superClass && superClass.prototype, {
-    constructor: {
-      value: subClass,
-      writable: true,
-      configurable: true
-    }
+  Object.defineProperty(subClass, "prototype", {
+    value: Object.create(superClass && superClass.prototype, {
+      constructor: {
+        value: subClass,
+        writable: true,
+        configurable: true
+      }
+    }),
+    writable: false
   });
   if (superClass) _setPrototypeOf(subClass, superClass);
 }
@@ -1716,7 +1739,8 @@ function mixin(dest, source, copyFunc) {
     // toString() method that source inherited from Object.prototype
     s = source[name];
 
-    if (!(name in dest) || dest[name] !== s && (!(name in empty) || empty[name] !== s)) {
+    if (!(name in dest) || // @ts-ignore
+    dest[name] !== s && (!(name in empty) || empty[name] !== s)) {
       dest[name] = copyFunc ? copyFunc(s) : s;
     }
   }
@@ -2363,33 +2387,25 @@ function _fetchConfigFile() {
           case 2:
             result = _context3.sent;
 
-            if (!(typeof result !== 'string')) {
-              _context3.next = 5;
-              break;
-            }
-
-            throw new Error("Error opening location: ".concat(location));
-
-          case 5:
             if (!isUriLocation(location)) {
-              _context3.next = 7;
+              _context3.next = 5;
               break;
             }
 
             return _context3.abrupt("return", parseJb1(result, location.uri));
 
-          case 7:
+          case 5:
             if (!isLocalPathLocation(location)) {
-              _context3.next = 9;
+              _context3.next = 7;
               break;
             }
 
             return _context3.abrupt("return", parseJb1(result, location.localPath));
 
-          case 9:
+          case 7:
             return _context3.abrupt("return", parseJb1(result));
 
-          case 10:
+          case 8:
           case "end":
             return _context3.stop();
         }
@@ -3076,9 +3092,7 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
   jb2TrackConfig.adapter = guessAdapter({
     uri: urlTemplate,
     locationType: 'UriLocation'
-  }, undefined, function () {
-    return urlTemplate;
-  });
+  }, undefined, urlTemplate);
 
   if (!jb2TrackConfig.adapter) {
     throw new Error('Could not determine adapter');
@@ -3186,6 +3200,22 @@ var LegacyJBrowsePlugin = /*#__PURE__*/function (_Plugin) {
           }
         });
       });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /trackData.jsonz?$/i;
+          var adapterName = 'NCListAdapter';
+          var fileName = getFileName(file);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              rootUrlTemplate: file
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
       pluginManager.addTextSearchAdapterType(function () {
         return new TextSearchAdapterType({
           name: 'JBrowse1TextSearchAdapter',