@jbrowse/plugin-config 1.5.0 → 1.5.4

package/dist/RefNameAliasAdapter/RefNameAliasAdapter.d.ts

@@ -1,13 +1,8 @@
-import { BaseRefNameAliasAdapter, Alias, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { ConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
-import MyConfigAdapterSchema from './configSchema';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import { BaseRefNameAliasAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 export default class RefNameAliasAdapter extends BaseAdapter implements BaseRefNameAliasAdapter {
-    private location;
-    private promise;
-    constructor(config: ConfigurationModel<typeof MyConfigAdapterSchema>, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    private downloadResults;
-    getRefNameAliases(): Promise<Alias[]>;
+    getRefNameAliases(): Promise<{
+        refName: string;
+        aliases: string[];
+    }[]>;
     freeResources(): Promise<void>;
 }

package/dist/plugin-config.cjs.development.js

@@ -35,11 +35,6 @@ var DeleteIcon = _interopDefault(require('@material-ui/icons/Delete'));
 var AddIcon = _interopDefault(require('@material-ui/icons/Add'));
 var RadioButtonUncheckedIcon = _interopDefault(require('@material-ui/icons/RadioButtonUnchecked'));
 var jexlStrings = require('@jbrowse/core/util/jexlStrings');
-var FormControl = _interopDefault(require('@material-ui/core/FormControl'));
-var FormHelperText = _interopDefault(require('@material-ui/core/FormHelperText'));
-var InputLabel = _interopDefault(require('@material-ui/core/InputLabel'));
-var Tooltip = _interopDefault(require('@material-ui/core/Tooltip'));
-var IconButton = _interopDefault(require('@material-ui/core/IconButton'));
 var HelpIcon = _interopDefault(require('@material-ui/icons/Help'));
 var ReactPropTypes = _interopDefault(require('prop-types'));
 var TextField = _interopDefault(require('@material-ui/core/TextField'));
@@ -52,14 +47,9 @@ function ownKeys(object, enumerableOnly) {
 
   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;
@@ -67,19 +57,12 @@ 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;
@@ -140,6 +123,9 @@ 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;
 }
 
@@ -181,12 +167,15 @@ 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);
 }
@@ -266,7 +255,7 @@ function _superPropBase(object, property) {
   return object;
 }
 
-function _get(target, property, receiver) {
+function _get() {
   if (typeof Reflect !== "undefined" && Reflect.get) {
     _get = Reflect.get;
   } else {
@@ -277,14 +266,14 @@ function _get(target, property, receiver) {
       var desc = Object.getOwnPropertyDescriptor(base, property);
 
       if (desc.get) {
-        return desc.get.call(receiver);
+        return desc.get.call(arguments.length < 3 ? target : receiver);
       }
 
       return desc.value;
     };
   }
 
-  return _get(target, property, receiver || target);
+  return _get.apply(this, arguments);
 }
 
 function _slicedToArray(arr, i) {
@@ -1306,7 +1295,9 @@ var FromConfigAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
     }
   }, {
     key: "freeResources",
-    value: function freeResources() {}
+    value: function
+      /* { region } */
+    freeResources() {}
   }], [{
     key: "makeFeatures",
     value: function makeFeatures(fdata) {
@@ -1458,7 +1449,9 @@ var FromConfigRegionsAdapter = /*#__PURE__*/function (_BaseAdapter) {
     }()
   }, {
     key: "freeResources",
-    value: function freeResources() {}
+    value: function
+      /* { region } */
+    freeResources() {}
   }]);
 
   return FromConfigRegionsAdapter;
@@ -1608,7 +1601,9 @@ var FromConfigSequenceAdapter = /*#__PURE__*/function (_FromConfigAdapter) {
 
   }, {
     key: "freeResources",
-    value: function freeResources() {}
+    value: function
+      /* { region } */
+    freeResources() {}
   }]);
 
   return FromConfigSequenceAdapter;
@@ -1659,30 +1654,35 @@ var RefNameAliasAdapter = /*#__PURE__*/function (_BaseAdapter) {
 
   var _super = /*#__PURE__*/_createSuper(RefNameAliasAdapter);
 
-  function RefNameAliasAdapter(config, getSubAdapter, pluginManager) {
-    var _this;
-
+  function RefNameAliasAdapter() {
     _classCallCheck(this, RefNameAliasAdapter);
 
-    _this = _super.call(this, config, getSubAdapter, pluginManager);
-    _this.location = io.openLocation(configuration.readConfObject(config, 'location'), _this.pluginManager);
-    _this.promise = _this.downloadResults();
-    return _this;
+    return _super.apply(this, arguments);
   }
 
   _createClass(RefNameAliasAdapter, [{
-    key: "downloadResults",
+    key: "getRefNameAliases",
     value: function () {
-      var _downloadResults = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee() {
-        var results;
+      var _getRefNameAliases = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee() {
+        var loc, results;
         return runtime_1.wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
-                _context.next = 2;
-                return this.location.readFile('utf8');
+                loc = configuration.readConfObject(this.config, 'location');
+
+                if (!(loc.uri === '' || loc.uri === '/path/to/my/aliases.txt')) {
+                  _context.next = 3;
+                  break;
+                }
+
+                return _context.abrupt("return", []);
+
+              case 3:
+                _context.next = 5;
+                return io.openLocation(loc).readFile('utf8');
 
-              case 2:
+              case 5:
                 results = _context.sent;
                 return _context.abrupt("return", results.trim().split('\n').map(function (row) {
                   var _row$split = row.split('\t'),
@@ -1696,7 +1696,7 @@ var RefNameAliasAdapter = /*#__PURE__*/function (_BaseAdapter) {
                   };
                 }));
 
-              case 4:
+              case 7:
               case "end":
                 return _context.stop();
             }
@@ -1704,17 +1704,12 @@ var RefNameAliasAdapter = /*#__PURE__*/function (_BaseAdapter) {
         }, _callee, this);
       }));
 
-      function downloadResults() {
-        return _downloadResults.apply(this, arguments);
+      function getRefNameAliases() {
+        return _getRefNameAliases.apply(this, arguments);
       }
 
-      return downloadResults;
+      return getRefNameAliases;
     }()
-  }, {
-    key: "getRefNameAliases",
-    value: function getRefNameAliases() {
-      return this.promise;
-    }
   }, {
     key: "freeResources",
     value: function () {
@@ -1833,28 +1828,52 @@ var _default = /*#__PURE__*/function (_Plugin) {
         return new AdapterType({
           name: 'FromConfigAdapter',
           configSchema: configSchema$1,
-          AdapterClass: FromConfigAdapter
+          AdapterClass: FromConfigAdapter,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          }
         });
       });
       pluginManager.addAdapterType(function () {
         return new AdapterType({
           name: 'FromConfigRegionsAdapter',
           configSchema: regionsConfigSchema,
-          AdapterClass: FromConfigRegionsAdapter
+          AdapterClass: FromConfigRegionsAdapter,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          }
         });
       });
       pluginManager.addAdapterType(function () {
         return new AdapterType({
           name: 'FromConfigSequenceAdapter',
           configSchema: sequenceConfigSchema,
-          AdapterClass: FromConfigSequenceAdapter
+          AdapterClass: FromConfigSequenceAdapter,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          }
         });
       });
       pluginManager.addAdapterType(function () {
         return new AdapterType({
           name: 'RefNameAliasAdapter',
           configSchema: refNameAliasAdapterConfigSchema,
-          AdapterClass: RefNameAliasAdapter
+          AdapterClass: RefNameAliasAdapter,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          }
         });
       });
       pluginManager.addWidgetType(function () {
@@ -1929,7 +1948,7 @@ var fontSize$1 = '12px'; // Optimize by using system default fonts:
 // https://css-tricks.com/snippets/css/font-stacks/
 
 var fontFamily$1 = 'Consolas, "Andale Mono WT", "Andale Mono", "Lucida Console", "Lucida Sans Typewriter", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Liberation Mono", "Nimbus Mono L", Monaco, "Courier New", Courier, monospace';
-var useStyles$2 = /*#__PURE__*/styles.makeStyles(function (theme) {
+var useStyles$2 = /*#__PURE__*/core.makeStyles(function (theme) {
   return {
     callbackEditor: {
       marginTop: '16px',
@@ -1970,7 +1989,7 @@ function CallbackEditor(_ref) {
   }, [debouncedCode, slot]); // if default value is a callback, will have to remove jexl:
   // do this last
 
-  return /*#__PURE__*/React__default.createElement(React__default.Fragment, null, /*#__PURE__*/React__default.createElement(FormControl, null, /*#__PURE__*/React__default.createElement(InputLabel, {
+  return /*#__PURE__*/React__default.createElement(React__default.Fragment, null, /*#__PURE__*/React__default.createElement(core.FormControl, null, /*#__PURE__*/React__default.createElement(core.InputLabel, {
     shrink: true,
     htmlFor: "callback-editor"
   }, slot.name), /*#__PURE__*/React__default.createElement(Editor, {
@@ -1986,10 +2005,10 @@ function CallbackEditor(_ref) {
     style: {
       background: error ? '#fdd' : undefined
     }
-  }), /*#__PURE__*/React__default.createElement(FormHelperText, null, slot.description)), /*#__PURE__*/React__default.createElement(Tooltip, {
+  }), /*#__PURE__*/React__default.createElement(core.FormHelperText, null, slot.description)), /*#__PURE__*/React__default.createElement(core.Tooltip, {
     title: /*#__PURE__*/React__default.createElement("div", null, "Callbacks are written in Jexl format. Click to learn more.", /*#__PURE__*/React__default.createElement("br", null), " Names of available context items: ", slot.contextVariable),
     arrow: true
-  }, /*#__PURE__*/React__default.createElement(IconButton, {
+  }, /*#__PURE__*/React__default.createElement(core.IconButton, {
     color: "primary",
     onClick: function onClick() {
       var newWindow = window.open('https://github.com/TomFrost/Jexl', '_blank', 'noopener,noreferrer');
@@ -2017,7 +2036,7 @@ function serializeColor(color) {
         g = color.g,
         b = color.b,
         a = color.a;
-    return "rgb(".concat(r, ",").concat(g, ",").concat(b, ",").concat(a, ")");
+    return a === undefined ? "rgb(".concat(r, ",").concat(g, ",").concat(b, ")") : "rgba(".concat(r, ",").concat(g, ",").concat(b, ",").concat(a, ")");
   }
 
   return color;