@jbrowse/plugin-variants 1.6.8 → 1.7.1

package/dist/index.js

@@ -1,8 +1,216 @@
+"use strict";
 
-'use strict'
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
-if (process.env.NODE_ENV === 'production') {
-  module.exports = require('./plugin-variants.cjs.production.min.js')
-} else {
-  module.exports = require('./plugin-variants.cjs.development.js')
-}
+var _typeof = require("@babel/runtime/helpers/typeof");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+Object.defineProperty(exports, "VcfFeature", {
+  enumerable: true,
+  get: function get() {
+    return _VcfFeature["default"];
+  }
+});
+exports["default"] = void 0;
+
+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 _configuration = require("@jbrowse/core/configuration");
+
+var _AdapterType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+
+var _DisplayType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
+
+var _models = require("@jbrowse/core/pluggableElementTypes/models");
+
+var _TrackType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
+
+var _WidgetType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
+
+var _Plugin2 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
+
+var _pluginLinearGenomeView = require("@jbrowse/plugin-linear-genome-view");
+
+var _ChordVariantDisplay = _interopRequireDefault(require("./ChordVariantDisplay"));
+
+var _LinearVariantDisplay = require("./LinearVariantDisplay");
+
+var _StructuralVariantChordRenderer = _interopRequireDefault(require("./StructuralVariantChordRenderer"));
+
+var _VariantFeatureWidget = require("./VariantFeatureWidget");
+
+var _VcfTabixAdapter = require("./VcfTabixAdapter");
+
+var _VcfAdapter = require("./VcfAdapter");
+
+var _tracks = require("@jbrowse/core/util/tracks");
+
+var _VcfFeature = _interopRequireDefault(require("./VcfTabixAdapter/VcfFeature"));
+
+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 || _typeof(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; }
+
+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 VariantsPlugin = /*#__PURE__*/function (_Plugin) {
+  (0, _inherits2["default"])(VariantsPlugin, _Plugin);
+
+  var _super = _createSuper(VariantsPlugin);
+
+  function VariantsPlugin() {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, VariantsPlugin);
+
+    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", 'VariantsPlugin');
+    return _this;
+  }
+
+  (0, _createClass2["default"])(VariantsPlugin, [{
+    key: "install",
+    value: function install(pluginManager) {
+      pluginManager.addAdapterType(function () {
+        return new _AdapterType["default"]({
+          name: 'VcfTabixAdapter',
+          configSchema: _VcfTabixAdapter.configSchema,
+          getAdapterClass: function getAdapterClass() {
+            return Promise.resolve().then(function () {
+              return _interopRequireWildcard(require('./VcfTabixAdapter/VcfTabixAdapter'));
+            }).then(function (r) {
+              return r["default"];
+            });
+          }
+        });
+      });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.vcf\.b?gz$/i;
+          var adapterName = 'VcfTabixAdapter';
+          var fileName = (0, _tracks.getFileName)(file);
+          var indexName = index && (0, _tracks.getFileName)(index);
+          var obj = {
+            type: adapterName,
+            vcfGzLocation: file,
+            index: {
+              location: index || (0, _tracks.makeIndex)(file, '.tbi'),
+              indexType: (0, _tracks.makeIndexType)(indexName, 'CSI', 'TBI')
+            }
+          };
+
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj;
+          } else if (adapterHint === adapterName) {
+            return obj;
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
+        return function (adapterName) {
+          if (adapterName === 'VcfTabixAdapter' || adapterName === 'VcfAdapter') {
+            return 'VariantTrack';
+          }
+
+          return trackTypeGuesser(adapterName);
+        };
+      });
+      pluginManager.addAdapterType(function () {
+        return new _AdapterType["default"]({
+          name: 'VcfAdapter',
+          configSchema: _VcfAdapter.configSchema,
+          getAdapterClass: function getAdapterClass() {
+            return Promise.resolve().then(function () {
+              return _interopRequireWildcard(require('./VcfAdapter/VcfAdapter'));
+            }).then(function (r) {
+              return r["default"];
+            });
+          }
+        });
+      });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.vcf$/i;
+          var adapterName = 'VcfAdapter';
+          var fileName = (0, _tracks.getFileName)(file);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              vcfLocation: file
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addRendererType(function () {
+        return pluginManager.jbrequire(_StructuralVariantChordRenderer["default"]);
+      });
+      pluginManager.addTrackType(function () {
+        var configSchema = (0, _configuration.ConfigurationSchema)('VariantTrack', {}, {
+          baseConfiguration: (0, _models.createBaseTrackConfig)(pluginManager)
+        });
+        return new _TrackType["default"]({
+          name: 'VariantTrack',
+          configSchema: configSchema,
+          stateModel: (0, _models.createBaseTrackModel)(pluginManager, 'VariantTrack', configSchema)
+        });
+      });
+      pluginManager.addDisplayType(function () {
+        return pluginManager.jbrequire(_ChordVariantDisplay["default"]);
+      });
+      pluginManager.addDisplayType(function () {
+        var configSchema = (0, _LinearVariantDisplay.configSchemaFactory)(pluginManager);
+        return new _DisplayType["default"]({
+          name: 'LinearVariantDisplay',
+          configSchema: configSchema,
+          stateModel: (0, _LinearVariantDisplay.modelFactory)(configSchema),
+          trackType: 'VariantTrack',
+          viewType: 'LinearGenomeView',
+          ReactComponent: _pluginLinearGenomeView.BaseLinearDisplayComponent
+        });
+      });
+      pluginManager.addWidgetType(function () {
+        return new _WidgetType["default"]({
+          name: 'VariantFeatureWidget',
+          heading: 'Feature details',
+          configSchema: _VariantFeatureWidget.configSchema,
+          stateModel: (0, _VariantFeatureWidget.stateModelFactory)(pluginManager),
+          ReactComponent: /*#__PURE__*/(0, _react.lazy)(function () {
+            return Promise.resolve().then(function () {
+              return _interopRequireWildcard(require('./VariantFeatureWidget/VariantFeatureWidget'));
+            });
+          })
+        });
+      });
+    }
+  }]);
+  return VariantsPlugin;
+}(_Plugin2["default"]);
+
+exports["default"] = VariantsPlugin;

package/dist/index.test.js

@@ -0,0 +1,37 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
+
+var _pluginAlignments = _interopRequireDefault(require("@jbrowse/plugin-alignments"));
+
+var _pluginSvg = _interopRequireDefault(require("@jbrowse/plugin-svg"));
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _ = _interopRequireDefault(require("."));
+
+test('plugin in a stock JBrowse', function () {
+  console.warn = jest.fn();
+  var pluginManager = new _PluginManager["default"]([new _["default"](), new _pluginAlignments["default"](), new _pluginSvg["default"]()]);
+  pluginManager.createPluggableElements();
+  pluginManager.configure();
+  expect(function () {
+    return pluginManager.addPlugin(new _["default"]());
+  }).toThrow(/JBrowse already configured, cannot add plugins/);
+  var VcfTabixAdapter = pluginManager.getAdapterType('VcfTabixAdapter');
+  var config = VcfTabixAdapter.configSchema.create({
+    type: 'VcfTabixAdapter'
+  });
+  expect((0, _mobxStateTree.getSnapshot)(config)).toMatchSnapshot();
+  var VariantTrack = pluginManager.getTrackType('VariantTrack');
+  var config2 = VariantTrack.configSchema.create({
+    type: 'VariantTrack',
+    trackId: 'trackId0',
+    adapter: {
+      type: 'VcfTabixAdapter'
+    }
+  });
+  expect((0, _mobxStateTree.getSnapshot)(config2)).toMatchSnapshot();
+});

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "1.6.8",
+  "version": "1.7.1",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -18,21 +18,19 @@
   "distMain": "dist/index.js",
   "srcMain": "src/index.ts",
   "main": "dist/index.js",
-  "distModule": "dist/plugin-variants.esm.js",
-  "module": "dist/plugin-variants.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/variants",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js"
+    "useSrc": "node ../../scripts/useSrc.js",
+    "postbuild": "tsc --build tsconfig.build.json"
   },
   "dependencies": {
     "@flatten-js/interval-tree": "^1.0.15",
@@ -58,5 +56,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "585e522096651ef4afb188366bb46d723439dc1b"
+  "gitHead": "6da232090c90f22ac96fd464c33082c89b8da14b"
 }

package/dist/LinearVariantDisplay/configSchema.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/VariantFeatureWidget/VariantFeatureWidget.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/index.test.d.ts

@@ -1 +0,0 @@
-export {};