@jbrowse/plugin-config 1.6.7 → 1.7.0

package/dist/RefNameAliasAdapter/RefNameAliasAdapter.js

@@ -0,0 +1,125 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
+var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
+
+var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
+
+var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
+
+var _BaseAdapter2 = require("@jbrowse/core/data_adapters/BaseAdapter");
+
+var _io = require("@jbrowse/core/util/io");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2["default"])(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2["default"])(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2["default"])(this, result); }; }
+
+function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
+
+var RefNameAliasAdapter = /*#__PURE__*/function (_BaseAdapter) {
+  (0, _inherits2["default"])(RefNameAliasAdapter, _BaseAdapter);
+
+  var _super = _createSuper(RefNameAliasAdapter);
+
+  function RefNameAliasAdapter() {
+    (0, _classCallCheck2["default"])(this, RefNameAliasAdapter);
+    return _super.apply(this, arguments);
+  }
+
+  (0, _createClass2["default"])(RefNameAliasAdapter, [{
+    key: "getRefNameAliases",
+    value: function () {
+      var _getRefNameAliases = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+        var loc, results, refColumn;
+        return _regenerator["default"].wrap(function _callee$(_context) {
+          while (1) {
+            switch (_context.prev = _context.next) {
+              case 0:
+                loc = (0, _configuration.readConfObject)(this.config, 'location');
+
+                if (!(loc.uri === '' || loc.uri === '/path/to/my/aliases.txt')) {
+                  _context.next = 3;
+                  break;
+                }
+
+                return _context.abrupt("return", []);
+
+              case 3:
+                _context.next = 5;
+                return (0, _io.openLocation)(loc).readFile('utf8');
+
+              case 5:
+                results = _context.sent;
+                refColumn = (0, _configuration.readConfObject)(this.config, 'refNameColumn');
+                return _context.abrupt("return", results.trim().split('\n').filter(function (f) {
+                  return !!f && !f.startsWith('#');
+                }).map(function (row) {
+                  var aliases = row.split('\t');
+
+                  var _aliases$splice = aliases.splice(refColumn, 1),
+                      _aliases$splice2 = (0, _slicedToArray2["default"])(_aliases$splice, 1),
+                      refName = _aliases$splice2[0];
+
+                  return {
+                    refName: refName,
+                    aliases: aliases
+                  };
+                }));
+
+              case 8:
+              case "end":
+                return _context.stop();
+            }
+          }
+        }, _callee, this);
+      }));
+
+      function getRefNameAliases() {
+        return _getRefNameAliases.apply(this, arguments);
+      }
+
+      return getRefNameAliases;
+    }()
+  }, {
+    key: "freeResources",
+    value: function () {
+      var _freeResources = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+        return _regenerator["default"].wrap(function _callee2$(_context2) {
+          while (1) {
+            switch (_context2.prev = _context2.next) {
+              case 0:
+              case "end":
+                return _context2.stop();
+            }
+          }
+        }, _callee2);
+      }));
+
+      function freeResources() {
+        return _freeResources.apply(this, arguments);
+      }
+
+      return freeResources;
+    }()
+  }]);
+  return RefNameAliasAdapter;
+}(_BaseAdapter2.BaseAdapter);
+
+exports["default"] = RefNameAliasAdapter;

package/dist/RefNameAliasAdapter/RefNameAliasAdapter.test.js

@@ -0,0 +1,41 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _RefNameAliasAdapter = _interopRequireDefault(require("./RefNameAliasAdapter"));
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));
+
+test('adapter can fetch a simple alias file', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+  var adapter, result;
+  return _regenerator["default"].wrap(function _callee$(_context) {
+    while (1) {
+      switch (_context.prev = _context.next) {
+        case 0:
+          adapter = new _RefNameAliasAdapter["default"](_configSchema["default"].create({
+            location: {
+              localPath: require.resolve('./test_data/simple_alias.txt'),
+              locationType: 'LocalPathLocation'
+            }
+          }));
+          _context.next = 3;
+          return adapter.getRefNameAliases();
+
+        case 3:
+          result = _context.sent;
+          expect(result[0].refName).toBe('chr1');
+          expect(result[0].aliases).toEqual(['1', 'NC_000001.10']);
+          expect(result[1].refName).toBe('chr2');
+          expect(result[1].aliases).toEqual(['2', 'NC_000002.11']);
+
+        case 8:
+        case "end":
+          return _context.stop();
+      }
+    }
+  }, _callee);
+})));

package/dist/RefNameAliasAdapter/configSchema.js

@@ -0,0 +1,26 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _default = (0, _configuration.ConfigurationSchema)('RefNameAliasAdapter', {
+  location: {
+    type: 'fileLocation',
+    defaultValue: {
+      uri: '/path/to/my/aliases.txt',
+      locationType: 'UriLocation'
+    }
+  },
+  refNameColumn: {
+    type: 'number',
+    defaultValue: 0
+  }
+}, {
+  explicitlyTyped: true
+});
+
+exports["default"] = _default;

package/dist/RefNameAliasAdapter/index.js

@@ -0,0 +1,23 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+Object.defineProperty(exports, "AdapterClass", {
+  enumerable: true,
+  get: function get() {
+    return _RefNameAliasAdapter["default"];
+  }
+});
+Object.defineProperty(exports, "configSchema", {
+  enumerable: true,
+  get: function get() {
+    return _configSchema["default"];
+  }
+});
+
+var _RefNameAliasAdapter = _interopRequireDefault(require("./RefNameAliasAdapter"));
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));

package/dist/index.js

@@ -1,8 +1,152 @@
+"use strict";
 
-'use strict'
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
-if (process.env.NODE_ENV === 'production') {
-  module.exports = require('./plugin-config.cjs.production.min.js')
-} else {
-  module.exports = require('./plugin-config.cjs.development.js')
-}
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.ConfigurationEditor = void 0;
+Object.defineProperty(exports, "JsonEditor", {
+  enumerable: true,
+  get: function get() {
+    return _JsonEditor["default"];
+  }
+});
+exports["default"] = void 0;
+
+var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
+
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
+var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
+
+var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
+
+var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
+
+var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _react = require("react");
+
+var _AdapterType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+
+var _WidgetType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
+
+var _Plugin2 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
+
+var _ConfigurationEditorWidget = require("./ConfigurationEditorWidget");
+
+var _FromConfigAdapter = require("./FromConfigAdapter");
+
+var _RefNameAliasAdapter = require("./RefNameAliasAdapter");
+
+var _JsonEditor = _interopRequireDefault(require("./ConfigurationEditorWidget/components/JsonEditor"));
+
+function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2["default"])(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2["default"])(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2["default"])(this, result); }; }
+
+function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
+
+function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
+
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || (0, _typeof2["default"])(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+
+var ConfigurationEditorComponent = /*#__PURE__*/(0, _react.lazy)(function () {
+  return Promise.resolve().then(function () {
+    return _interopRequireWildcard(require('./ConfigurationEditorWidget/components/ConfigurationEditor'));
+  });
+});
+exports.ConfigurationEditor = ConfigurationEditorComponent;
+
+var _default = /*#__PURE__*/function (_Plugin) {
+  (0, _inherits2["default"])(_default, _Plugin);
+
+  var _super = _createSuper(_default);
+
+  function _default() {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, _default);
+
+    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
+      args[_key] = arguments[_key];
+    }
+
+    _this = _super.call.apply(_super, [this].concat(args));
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "name", 'ConfigurationPlugin');
+    return _this;
+  }
+
+  (0, _createClass2["default"])(_default, [{
+    key: "install",
+    value: function install(pluginManager) {
+      pluginManager.addAdapterType(function () {
+        return new _AdapterType["default"]({
+          name: 'FromConfigAdapter',
+          configSchema: _FromConfigAdapter.configSchema,
+          AdapterClass: _FromConfigAdapter.AdapterClass,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          }
+        });
+      });
+      pluginManager.addAdapterType(function () {
+        return new _AdapterType["default"]({
+          name: 'FromConfigRegionsAdapter',
+          configSchema: _FromConfigAdapter.regionsConfigSchema,
+          AdapterClass: _FromConfigAdapter.RegionsAdapterClass,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          }
+        });
+      });
+      pluginManager.addAdapterType(function () {
+        return new _AdapterType["default"]({
+          name: 'FromConfigSequenceAdapter',
+          configSchema: _FromConfigAdapter.sequenceConfigSchema,
+          AdapterClass: _FromConfigAdapter.SequenceAdapterClass,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          }
+        });
+      });
+      pluginManager.addAdapterType(function () {
+        return new _AdapterType["default"]({
+          name: 'RefNameAliasAdapter',
+          configSchema: _RefNameAliasAdapter.configSchema,
+          AdapterClass: _RefNameAliasAdapter.AdapterClass,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          }
+        });
+      });
+      pluginManager.addWidgetType(function () {
+        return new _WidgetType["default"]({
+          name: 'ConfigurationEditorWidget',
+          HeadingComponent: _ConfigurationEditorWidget.HeadingComponent,
+          configSchema: _ConfigurationEditorWidget.configSchema,
+          stateModel: (0, _ConfigurationEditorWidget.stateModelFactory)(pluginManager),
+          ReactComponent: ConfigurationEditorComponent
+        });
+      });
+    }
+  }]);
+  return _default;
+}(_Plugin2["default"]);
+
+exports["default"] = _default;

package/dist/index.test.js

@@ -0,0 +1,41 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _ = _interopRequireDefault(require("."));
+
+describe('Config editing', function () {
+  var pluginManager;
+  beforeAll(function () {
+    var originalConsoleWarn = console.warn;
+    console.warn = jest.fn();
+    pluginManager = new _PluginManager["default"]([new _["default"]()]);
+    pluginManager.createPluggableElements();
+    pluginManager.configure();
+    console.warn = originalConsoleWarn;
+  });
+  it("won't add if already added", function () {
+    expect(function () {
+      return pluginManager.addPlugin(new _["default"]());
+    }).toThrow(/JBrowse already configured, cannot add plugins/);
+  });
+  it('adds config editor widget', function () {
+    var ConfigurationEditorWidget = pluginManager.getWidgetType('ConfigurationEditorWidget');
+    var config = ConfigurationEditorWidget.configSchema.create({
+      type: 'ConfigurationEditorWidget'
+    });
+    expect((0, _mobxStateTree.getSnapshot)(config)).toMatchSnapshot();
+  });
+  it('creates proper FromConfigAdapter', function () {
+    var adapter = pluginManager.getAdapterType('FromConfigAdapter');
+    var config = adapter.configSchema.create({
+      type: 'FromConfigAdapter',
+      adapterId: 'testFromConfigAdapterId'
+    });
+    expect((0, _mobxStateTree.getSnapshot)(config)).toMatchSnapshot();
+  });
+});

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-config",
-  "version": "1.6.7",
+  "version": "1.7.0",
   "description": "JBrowse 2 config utilities",
   "keywords": [
     "jbrowse",
@@ -18,15 +18,12 @@
   "distMain": "dist/index.js",
   "srcMain": "src/index.ts",
   "main": "dist/index.js",
-  "distModule": "dist/plugin-config.esm.js",
-  "module": "dist/plugin-config.esm.js",
   "files": [
     "dist",
     "src"
   ],
   "scripts": {
-    "start": "tsdx watch --verbose --noClean",
-    "build": "tsdx build",
+    "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
     "test": "cd ../..; jest plugins/config",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
@@ -55,5 +52,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "02012ec299c36647f755316571775d36b0fee5ec"
+  "gitHead": "cc13844074d11881d211342a6a7eea113561b70b"
 }

package/src/ConfigurationEditorWidget/components/ConfigurationEditor.js

@@ -125,24 +125,29 @@ const ConfigurationEditor = observer(({ model }) => {
   const key = model.target && readConfObject(model.target, 'trackId')
   const name = model.target && readConfObject(model.target, 'name')
   return (
-    <Accordion
-      key={key}
-      defaultExpanded
-      className={classes.accordion}
-      TransitionProps={{ unmountOnExit: true, timeout: 150 }}
-    >
-      <AccordionSummary
-        expandIcon={<ExpandMoreIcon className={classes.expandIcon} />}
-      >
-        <Typography>{name ? name : 'Configuration'}</Typography>
-      </AccordionSummary>
-      <AccordionDetails
-        className={classes.expansionPanelDetails}
-        data-testid="configEditor"
+    <>
+      <Accordion
+        key={key}
+        defaultExpanded
+        className={classes.accordion}
+        TransitionProps={{ unmountOnExit: true, timeout: 150 }}
       >
-        {!model.target ? 'no target set' : <Schema schema={model.target} />}
-      </AccordionDetails>
-    </Accordion>
+        <AccordionSummary
+          expandIcon={<ExpandMoreIcon className={classes.expandIcon} />}
+        >
+          <Typography>{name ? name : 'Configuration'}</Typography>
+        </AccordionSummary>
+        <AccordionDetails
+          className={classes.expansionPanelDetails}
+          data-testid="configEditor"
+        >
+          {!model.target ? 'no target set' : <Schema schema={model.target} />}
+        </AccordionDetails>
+      </Accordion>
+
+      {/* blank space at the bottom of screen allows scroll */}
+      <div style={{ height: 300 }} />
+    </>
   )
 })
 

package/src/ConfigurationEditorWidget/components/JsonEditor.js

@@ -31,8 +31,7 @@ function JsonEditor({ slot }) {
     } catch (e) {
       setError(e.message)
     }
-    // eslint-disable-next-line react-hooks/exhaustive-deps
-  }, [debouncedJson])
+  }, [debouncedJson, slot])
 
   return (
     <>