@jbrowse/plugin-circular-view 1.6.9 → 1.7.2

package/dist/BaseChordDisplay/models/BaseChordDisplayModel.js

@@ -0,0 +1,261 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.BaseChordDisplayModel = void 0;
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _models = require("@jbrowse/core/pluggableElementTypes/models");
+
+var _CircularChordRendererType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType"));
+
+var _util = require("@jbrowse/core/util");
+
+var _simpleFeature = require("@jbrowse/core/util/simpleFeature");
+
+var _tracks = require("@jbrowse/core/util/tracks");
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _renderReaction = _interopRequireDefault(require("./renderReaction"));
+
+function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
+
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2["default"])(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; }
+
+var BaseChordDisplayModel = _mobxStateTree.types.compose('BaseChordDisplay', _models.BaseDisplay, _mobxStateTree.types.model({
+  bezierRadiusRatio: 0.1,
+  assemblyName: _mobxStateTree.types.maybe(_mobxStateTree.types.string)
+}))["volatile"](function () {
+  return {
+    // NOTE: all this volatile stuff has to be filled in at once
+    // so that it stays consistent
+    filled: false,
+    reactElement: undefined,
+    data: undefined,
+    message: '',
+    renderingComponent: undefined,
+    refNameMap: undefined
+  };
+}).actions(function (self) {
+  var _getEnv = (0, _mobxStateTree.getEnv)(self),
+      pluginManager = _getEnv.pluginManager;
+
+  var track = self;
+  return {
+    onChordClick: function onChordClick(feature) {
+      (0, _configuration.getConf)(self, 'onChordClick', {
+        feature: feature,
+        track: track,
+        pluginManager: pluginManager
+      });
+    }
+  };
+}).views(function (self) {
+  return {
+    get blockDefinitions() {
+      var origSlices = (0, _util.getContainingView)(self).staticSlices;
+
+      if (!self.refNameMap) {
+        return origSlices;
+      }
+
+      var slices = JSON.parse(JSON.stringify(origSlices)); // eslint-disable-next-line @typescript-eslint/no-explicit-any
+
+      slices.forEach(function (slice) {
+        var regions = slice.region.elided ? slice.region.regions : [slice.region];
+        regions.forEach(function (region) {
+          var _self$refNameMap;
+
+          var renamed = (_self$refNameMap = self.refNameMap) === null || _self$refNameMap === void 0 ? void 0 : _self$refNameMap[region.refName];
+
+          if (renamed && region.refName !== renamed) {
+            region.refName = renamed;
+          }
+        });
+      });
+      return slices;
+    },
+
+    renderProps: function renderProps() {
+      var view = (0, _util.getContainingView)(self);
+      return _objectSpread(_objectSpread({}, (0, _tracks.getParentRenderProps)(self)), {}, {
+        rpcDriverName: self.rpcDriverName,
+        displayModel: self,
+        bezierRadius: view.radiusPx * self.bezierRadiusRatio,
+        radius: view.radiusPx,
+        blockDefinitions: this.blockDefinitions,
+        onChordClick: self.onChordClick
+      });
+    },
+
+    /**
+     * the pluggable element type object for this diplay's
+     * renderer
+     */
+    get rendererType() {
+      var display = self;
+
+      var _getEnv2 = (0, _mobxStateTree.getEnv)(self),
+          pluginManager = _getEnv2.pluginManager;
+
+      var ThisRendererType = pluginManager.getRendererType(self.rendererTypeName);
+
+      if (!ThisRendererType) {
+        throw new Error("renderer \"".concat(display.rendererTypeName, "\" not found"));
+      }
+
+      if (!ThisRendererType.ReactComponent) {
+        throw new Error("renderer ".concat(display.rendererTypeName, " has no ReactComponent, it may not be completely implemented yet"));
+      }
+
+      return ThisRendererType;
+    },
+
+    isCompatibleWithRenderer: function isCompatibleWithRenderer(renderer) {
+      return !!(renderer instanceof _CircularChordRendererType["default"]);
+    },
+
+    /**
+     * returns a string feature ID if the globally-selected object
+     * is probably a feature
+     */
+    get selectedFeatureId() {
+      if (!(0, _mobxStateTree.isAlive)(self)) {
+        return undefined;
+      }
+
+      var session = (0, _util.getSession)(self);
+
+      if (!session) {
+        return undefined;
+      }
+
+      var selection = session.selection; // does it quack like a feature?
+
+      if ((0, _simpleFeature.isFeature)(selection)) {
+        return selection.id();
+      }
+
+      return undefined;
+    }
+
+  };
+}).actions(function (self) {
+  return {
+    renderStarted: function renderStarted() {
+      self.filled = false;
+      self.message = '';
+      self.reactElement = undefined;
+      self.data = undefined;
+      self.error = undefined;
+      self.renderingComponent = undefined;
+    },
+    renderSuccess: function renderSuccess(_ref) {
+      var message = _ref.message,
+          data = _ref.data,
+          reactElement = _ref.reactElement,
+          renderingComponent = _ref.renderingComponent;
+
+      if (message) {
+        self.filled = false;
+        self.message = message;
+        self.reactElement = undefined;
+        self.data = undefined;
+        self.error = undefined;
+        self.renderingComponent = undefined;
+      } else {
+        self.filled = true;
+        self.message = '';
+        self.reactElement = reactElement;
+        self.data = data;
+        self.error = undefined;
+        self.renderingComponent = renderingComponent;
+      }
+    },
+    renderError: function renderError(error) {
+      console.error(error); // the rendering failed for some reason
+
+      self.filled = false;
+      self.message = '';
+      self.reactElement = undefined;
+      self.data = undefined;
+      self.error = error;
+      self.renderingComponent = undefined;
+    },
+    setRefNameMap: function setRefNameMap(refNameMap) {
+      self.refNameMap = refNameMap;
+    }
+  };
+}).actions(function (self) {
+  var _getEnv3 = (0, _mobxStateTree.getEnv)(self),
+      pluginManager = _getEnv3.pluginManager;
+
+  var _pluginManager$jbrequ = pluginManager.jbrequire(_renderReaction["default"]),
+      renderReactionData = _pluginManager$jbrequ.renderReactionData,
+      renderReactionEffect = _pluginManager$jbrequ.renderReactionEffect;
+
+  return {
+    afterAttach: function afterAttach() {
+      (0, _util.makeAbortableReaction)(self, renderReactionData, renderReactionEffect, {
+        name: "".concat(self.type, " ").concat(self.id, " rendering"),
+        // delay: self.renderDelay || 300,
+        fireImmediately: true
+      }, self.renderStarted, self.renderSuccess, self.renderError);
+      (0, _util.makeAbortableReaction)(self, function () {
+        return {
+          assemblyNames: (0, _tracks.getTrackAssemblyNames)(self.parentTrack),
+          adapter: (0, _configuration.getConf)((0, _mobxStateTree.getParent)(self, 2), 'adapter'),
+          assemblyManager: (0, _util.getSession)(self).assemblyManager
+        };
+      },
+      /*#__PURE__*/
+      // eslint-disable-next-line @typescript-eslint/no-explicit-any
+      function () {
+        var _ref3 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(_ref2, signal) {
+          var assemblyNames, adapter, assemblyManager;
+          return _regenerator["default"].wrap(function _callee$(_context) {
+            while (1) {
+              switch (_context.prev = _context.next) {
+                case 0:
+                  assemblyNames = _ref2.assemblyNames, adapter = _ref2.adapter, assemblyManager = _ref2.assemblyManager;
+                  return _context.abrupt("return", assemblyManager.getRefNameMapForAdapter(adapter, assemblyNames[0], {
+                    signal: signal,
+                    sessionId: (0, _tracks.getRpcSessionId)(self)
+                  }));
+
+                case 2:
+                case "end":
+                  return _context.stop();
+              }
+            }
+          }, _callee);
+        }));
+
+        return function (_x, _x2) {
+          return _ref3.apply(this, arguments);
+        };
+      }(), {
+        name: "".concat(self.type, " ").concat(self.id, " getting refNames"),
+        fireImmediately: true
+      }, function () {}, function (refNameMap) {
+        self.setRefNameMap(refNameMap);
+      }, function (error) {
+        console.error(error);
+        self.setError(error);
+      });
+    }
+  };
+});
+
+exports.BaseChordDisplayModel = BaseChordDisplayModel;

package/dist/BaseChordDisplay/models/baseChordDisplayConfig.d.ts

@@ -1,2 +1,2 @@
-declare const baseChordDisplayConfig: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export { baseChordDisplayConfig };
+declare const baseChordDisplayConfig: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export { baseChordDisplayConfig };

package/dist/BaseChordDisplay/models/baseChordDisplayConfig.js

@@ -0,0 +1,20 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.baseChordDisplayConfig = void 0;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var baseChordDisplayConfig = (0, _configuration.ConfigurationSchema)('BaseChordDisplay', {
+  onChordClick: {
+    type: 'boolean',
+    description: 'callback that should be run when a chord in the track is clicked',
+    defaultValue: false,
+    contextVariable: ['feature', 'track', 'pluginManager']
+  }
+}, {
+  explicitIdentifier: 'displayId'
+});
+exports.baseChordDisplayConfig = baseChordDisplayConfig;

package/dist/BaseChordDisplay/models/renderReaction.d.ts

@@ -1,30 +1,30 @@
-declare function _default({ jbrequire }: {
-    jbrequire: any;
-}): {
-    renderReactionData: (self: any) => {
-        rendererType: any;
-        rpcManager: any;
-        renderProps: any;
-        renderArgs: {
-            assemblyName: any;
-            adapterConfig: any;
-            rendererType: any;
-            regions: any;
-            blockDefinitions: any;
-            sessionId: any;
-            timeout: number;
-        };
-    };
-    renderReactionEffect: (props: any, signal: any, self: any) => Promise<{
-        message: any;
-        html?: undefined;
-        data?: undefined;
-        renderingComponent?: undefined;
-    } | {
-        html: any;
-        data: any;
-        renderingComponent: any;
-        message?: undefined;
-    }>;
-};
-export default _default;
+declare function _default({ jbrequire }: {
+    jbrequire: any;
+}): {
+    renderReactionData: (self: any) => {
+        rendererType: any;
+        rpcManager: any;
+        renderProps: any;
+        renderArgs: {
+            assemblyName: any;
+            adapterConfig: any;
+            rendererType: any;
+            regions: any;
+            blockDefinitions: any;
+            sessionId: any;
+            timeout: number;
+        };
+    };
+    renderReactionEffect: (props: any, signal: any, self: any) => Promise<{
+        message: any;
+        html?: undefined;
+        data?: undefined;
+        renderingComponent?: undefined;
+    } | {
+        html: any;
+        data: any;
+        renderingComponent: any;
+        message?: undefined;
+    }>;
+};
+export default _default;

package/dist/BaseChordDisplay/models/renderReaction.js

@@ -0,0 +1,142 @@
+"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 _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _objectWithoutProperties2 = _interopRequireDefault(require("@babel/runtime/helpers/objectWithoutProperties"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _excluded = ["html"];
+
+function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
+
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2["default"])(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; }
+
+var _default = function _default(_ref) {
+  var jbrequire = _ref.jbrequire;
+
+  var _jbrequire = jbrequire('@jbrowse/core/util/tracks'),
+      getRpcSessionId = _jbrequire.getRpcSessionId;
+
+  var _jbrequire2 = jbrequire('@jbrowse/core/util'),
+      getContainingView = _jbrequire2.getContainingView;
+
+  var _jbrequire3 = jbrequire('@jbrowse/core/util'),
+      getSession = _jbrequire3.getSession;
+
+  function renderReactionData(self) {
+    var _view$displayedRegion;
+
+    var view = getContainingView(self);
+    var rendererType = self.rendererType;
+
+    var _getSession = getSession(view),
+        rpcManager = _getSession.rpcManager;
+
+    return {
+      rendererType: rendererType,
+      rpcManager: rpcManager,
+      renderProps: self.renderProps(),
+      renderArgs: {
+        assemblyName: (_view$displayedRegion = view.displayedRegions[0]) === null || _view$displayedRegion === void 0 ? void 0 : _view$displayedRegion.assemblyName,
+        adapterConfig: JSON.parse(JSON.stringify(self.adapterConfig)),
+        rendererType: rendererType.name,
+        regions: JSON.parse(JSON.stringify(view.displayedRegions)),
+        blockDefinitions: self.blockDefinitions,
+        sessionId: getRpcSessionId(self),
+        timeout: 1000000
+      }
+    };
+  }
+
+  function renderReactionEffect(_x, _x2, _x3) {
+    return _renderReactionEffect.apply(this, arguments);
+  }
+
+  function _renderReactionEffect() {
+    _renderReactionEffect = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(props, signal, self) {
+      var rendererType, rpcManager, cannotBeRenderedReason, renderArgs, renderProps, _yield$rendererType$r, html, data;
+
+      return _regenerator["default"].wrap(function _callee$(_context) {
+        while (1) {
+          switch (_context.prev = _context.next) {
+            case 0:
+              if (props) {
+                _context.next = 2;
+                break;
+              }
+
+              throw new Error('cannot render with no props');
+
+            case 2:
+              rendererType = props.rendererType, rpcManager = props.rpcManager, cannotBeRenderedReason = props.cannotBeRenderedReason, renderArgs = props.renderArgs, renderProps = props.renderProps;
+
+              if (!cannotBeRenderedReason) {
+                _context.next = 5;
+                break;
+              }
+
+              return _context.abrupt("return", {
+                message: cannotBeRenderedReason
+              });
+
+            case 5:
+              if (!(!props.renderProps.radius || !props.renderArgs.regions || !props.renderArgs.regions.length)) {
+                _context.next = 7;
+                break;
+              }
+
+              return _context.abrupt("return", {
+                message: 'Skipping render'
+              });
+
+            case 7:
+              if (self.isCompatibleWithRenderer(rendererType)) {
+                _context.next = 9;
+                break;
+              }
+
+              throw new Error("renderer ".concat(rendererType.name, " is not compatible with this display type"));
+
+            case 9:
+              _context.next = 11;
+              return rendererType.renderInClient(rpcManager, _objectSpread(_objectSpread(_objectSpread({}, renderArgs), renderProps), {}, {
+                signal: signal
+              }));
+
+            case 11:
+              _yield$rendererType$r = _context.sent;
+              html = _yield$rendererType$r.html;
+              data = (0, _objectWithoutProperties2["default"])(_yield$rendererType$r, _excluded);
+              return _context.abrupt("return", {
+                html: html,
+                data: data,
+                renderingComponent: rendererType.ReactComponent
+              });
+
+            case 15:
+            case "end":
+              return _context.stop();
+          }
+        }
+      }, _callee);
+    }));
+    return _renderReactionEffect.apply(this, arguments);
+  }
+
+  return {
+    renderReactionData: renderReactionData,
+    renderReactionEffect: renderReactionEffect
+  };
+};
+
+exports["default"] = _default;

package/dist/CircularView/components/CircularView.d.ts

@@ -1,4 +1,4 @@
-export default CircularView;
-declare function CircularView({ model }: {
-    model: any;
-}): JSX.Element;
+export default CircularView;
+declare function CircularView({ model }: {
+    model: any;
+}): JSX.Element;