@jbrowse/core 1.7.11 → 2.1.0

package/pluggableElementTypes/models/BaseDisplayModel.js

@@ -1,115 +1,82 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
+Object.defineProperty(exports, "__esModule", { value: true });
 exports.BaseDisplay = void 0;
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _configuration = require("../../configuration");
-
-var _tracks = require("../../util/tracks");
-
-var _mst = require("../../util/types/mst");
-
-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 BaseDisplay = _mobxStateTree.types.model('BaseDisplay', {
-  id: _mst.ElementId,
-  type: _mobxStateTree.types.string,
-  rpcDriverName: _mobxStateTree.types.maybe(_mobxStateTree.types.string)
-}).volatile(function () {
-  return {
+/* eslint-disable @typescript-eslint/no-explicit-any */
+const mobx_state_tree_1 = require("mobx-state-tree");
+const configuration_1 = require("../../configuration");
+const tracks_1 = require("../../util/tracks");
+const mst_1 = require("../../util/types/mst");
+exports.BaseDisplay = mobx_state_tree_1.types
+    .model('BaseDisplay', {
+    id: mst_1.ElementId,
+    type: mobx_state_tree_1.types.string,
+    rpcDriverName: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
+})
+    .volatile(() => ({
     rendererTypeName: '',
-    error: undefined
-  };
-}).views(function (self) {
-  return {
+    error: undefined,
+}))
+    .views(self => ({
     get RenderingComponent() {
-      var _getEnv = (0, _mobxStateTree.getEnv)(self),
-          pluginManager = _getEnv.pluginManager;
-
-      var displayType = pluginManager.getDisplayType(self.type);
-      return displayType.ReactComponent;
+        const { pluginManager } = (0, mobx_state_tree_1.getEnv)(self);
+        const displayType = pluginManager.getDisplayType(self.type);
+        return displayType.ReactComponent;
     },
-
     get DisplayBlurb() {
-      return null;
+        return null;
     },
-
     get adapterConfig() {
-      return (0, _configuration.getConf)(this.parentTrack, 'adapter');
+        return (0, configuration_1.getConf)(this.parentTrack, 'adapter');
     },
-
     get parentTrack() {
-      var track = (0, _mobxStateTree.getParent)(self);
-
-      while (!(track.configuration && (0, _configuration.getConf)(track, 'trackId'))) {
-        if ((0, _mobxStateTree.isRoot)(track)) {
-          throw new Error("No parent track found for ".concat(self.type, " ").concat(self.id));
+        let track = (0, mobx_state_tree_1.getParent)(self);
+        while (!(track.configuration && (0, configuration_1.getConf)(track, 'trackId'))) {
+            if ((0, mobx_state_tree_1.isRoot)(track)) {
+                throw new Error(`No parent track found for ${self.type} ${self.id}`);
+            }
+            track = (0, mobx_state_tree_1.getParent)(track);
         }
-
-        track = (0, _mobxStateTree.getParent)(track);
-      }
-
-      return track;
+        return track;
     },
-
     /**
      * the react props that are passed to the Renderer when data
      * is rendered in this display
      */
-    renderProps: function renderProps() {
-      return _objectSpread(_objectSpread({}, (0, _tracks.getParentRenderProps)(self)), {}, {
-        rpcDriverName: self.rpcDriverName,
-        displayModel: self
-      });
+    renderProps() {
+        return {
+            ...(0, tracks_1.getParentRenderProps)(self),
+            rpcDriverName: self.rpcDriverName,
+            displayModel: self,
+        };
     },
-
     /**
      * the pluggable element type object for this display's
      * renderer
      */
     get rendererType() {
-      var _getEnv2 = (0, _mobxStateTree.getEnv)(self),
-          pluginManager = _getEnv2.pluginManager;
-
-      var RendererType = pluginManager.getRendererType(self.rendererTypeName);
-
-      if (!RendererType) {
-        throw new Error("renderer \"".concat(self.rendererTypeName, "\" not found"));
-      }
-
-      if (!RendererType.ReactComponent) {
-        throw new Error("renderer ".concat(self.rendererTypeName, " has no ReactComponent, it may not be completely implemented yet"));
-      }
-
-      return RendererType;
+        const { pluginManager } = (0, mobx_state_tree_1.getEnv)(self);
+        const RendererType = pluginManager.getRendererType(self.rendererTypeName);
+        if (!RendererType) {
+            throw new Error(`renderer "${self.rendererTypeName}" not found`);
+        }
+        if (!RendererType.ReactComponent) {
+            throw new Error(`renderer ${self.rendererTypeName} has no ReactComponent, it may not be completely implemented yet`);
+        }
+        return RendererType;
     },
-
     /**
      * if a display-level message should be displayed instead,
      * make this return a react component
      */
     get DisplayMessageComponent() {
-      return undefined;
+        return undefined;
     },
-
-    trackMenuItems: function trackMenuItems() {
-      return [];
+    trackMenuItems() {
+        return [];
     },
-
     get viewMenuActions() {
-      return [];
+        return [];
     },
-
     /**
      * @param region -
      * @returns falsy if the region is fine to try rendering. Otherwise,
@@ -117,21 +84,17 @@ var BaseDisplay = _mobxStateTree.types.model('BaseDisplay', {
      *  string of text describes why it cannot be rendered
      *  react node allows user to force load at current setting
      */
-    regionCannotBeRendered: function regionCannotBeRendered() {
-      return undefined;
-    }
-  };
-}).actions(function (self) {
-  return {
-    setError: function setError(error) {
-      self.error = error;
+    regionCannotBeRendered( /* region */) {
+        return undefined;
+    },
+}))
+    .actions(self => ({
+    setError(error) {
+        self.error = error;
     },
-    setRpcDriverName: function setRpcDriverName(rpcDriverName) {
-      self.rpcDriverName = rpcDriverName;
+    setRpcDriverName(rpcDriverName) {
+        self.rpcDriverName = rpcDriverName;
     },
     // base display reload does nothing, see specialized displays for details
-    reload: function reload() {}
-  };
-});
-
-exports.BaseDisplay = BaseDisplay;
+    reload() { },
+}));

package/pluggableElementTypes/models/BaseTrackModel.d.ts

@@ -21,7 +21,7 @@ export declare function createBaseTrackModel(pluginManager: PluginManager, track
     activateConfigurationUI(): void;
     showDisplay(displayId: string, initialSnapshot?: {}): void;
     hideDisplay(displayId: string): number;
-    replaceDisplay(oldDisplayId: string, newDisplayId: string, initialSnapshot?: {}): void;
+    replaceDisplay(oldId: string, newId: string, initialSnapshot?: {}): void;
 } & {
     trackMenuItems(): MenuItem[];
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/pluggableElementTypes/models/BaseTrackModel.js

@@ -1,208 +1,147 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.createBaseTrackModel = createBaseTrackModel;
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-var _mobx = require("mobx");
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _configuration = require("../../configuration");
-
-var _util = require("../../util");
-
-var _types = require("../../util/types");
-
-var _mst = require("../../util/types/mst");
-
-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; }
-
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.createBaseTrackModel = void 0;
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const configuration_1 = require("../../configuration");
+const util_1 = require("../../util");
+const types_1 = require("../../util/types");
+const mst_1 = require("../../util/types/mst");
 // these MST models only exist for tracks that are *shown*.
 // they should contain only UI state for the track, and have
 // a reference to a track configuration (stored under
 // session.configuration.assemblies.get(assemblyName).tracks).
 // note that multiple displayed tracks could use the same configuration.
 function createBaseTrackModel(pluginManager, trackType, baseTrackConfig) {
-  return _mobxStateTree.types.model(trackType, {
-    id: _mst.ElementId,
-    type: _mobxStateTree.types.literal(trackType),
-    configuration: (0, _configuration.ConfigurationReference)(baseTrackConfig),
-    displays: _mobxStateTree.types.array(pluginManager.pluggableMstType('display', 'stateModel'))
-  }).views(function (self) {
-    return {
-      get rpcSessionId() {
-        return self.configuration.trackId;
-      },
-
-      get name() {
-        return (0, _configuration.getConf)(self, 'name');
-      },
-
-      get textSearchAdapter() {
-        return (0, _configuration.getConf)(self, 'textSearchAdapter');
-      },
-
-      /**
-       * the PluggableElementType for the currently defined adapter
-       */
-      get adapterType() {
-        var adapterConfig = (0, _configuration.getConf)(self, 'adapter');
-
-        var _getEnv = (0, _mobxStateTree.getEnv)(self),
-            pm = _getEnv.pluginManager;
-
-        if (!adapterConfig) {
-          throw new Error("no adapter configuration provided for ".concat(self.type));
-        }
-
-        var adapterType = pm.getAdapterType(adapterConfig.type);
-
-        if (!adapterType) {
-          throw new Error("unknown adapter type ".concat(adapterConfig.type));
-        }
-
-        return adapterType;
-      },
-
-      get viewMenuActions() {
-        var menuItems = [];
-        self.displays.forEach(function (display) {
-          menuItems.push.apply(menuItems, (0, _toConsumableArray2.default)(display.viewMenuActions));
-        });
-        return menuItems;
-      },
-
-      get canConfigure() {
-        var session = (0, _util.getSession)(self);
-        return (0, _types.isSessionModelWithConfigEditing)(session) && ( // @ts-ignore
-        session.adminMode || // @ts-ignore
-        session.sessionTracks.find(function (track) {
-          return track.trackId === self.configuration.trackId;
-        }));
-      }
-
-    };
-  }).actions(function (self) {
-    return {
-      activateConfigurationUI: function activateConfigurationUI() {
-        var session = (0, _util.getSession)(self);
-        var view = (0, _util.getContainingView)(self);
-
-        if ((0, _types.isSessionModelWithConfigEditing)(session)) {
-          // @ts-ignore
-          var trackConf = session.editTrackConfiguration(self.configuration);
-
-          if (trackConf && trackConf !== self.configuration) {
-            // @ts-ignore
-            view.hideTrack(self.configuration); // @ts-ignore
-
-            view.showTrack(trackConf);
-          }
-        }
-      },
-      showDisplay: function showDisplay(displayId) {
-        var initialSnapshot = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
-        var displayTypeConfigSchema = pluginManager.pluggableConfigSchemaType('display');
-        var configuration = (0, _mobxStateTree.resolveIdentifier)(displayTypeConfigSchema, (0, _mobxStateTree.getRoot)(self), displayId);
-        var displayType = pluginManager.getDisplayType(configuration.type);
-
-        if (!displayType) {
-          throw new Error("unknown display type ".concat(configuration.type));
-        }
-
-        var display = displayType.stateModel.create(_objectSpread(_objectSpread({}, initialSnapshot), {}, {
-          type: configuration.type,
-          configuration: configuration
-        }));
-        self.displays.push(display);
-      },
-      hideDisplay: function hideDisplay(displayId) {
-        var displayTypeConfigSchema = pluginManager.pluggableConfigSchemaType('display');
-        var configuration = (0, _mobxStateTree.resolveIdentifier)(displayTypeConfigSchema, (0, _mobxStateTree.getRoot)(self), displayId); // if we have any displays with that configuration, turn them off
-
-        var shownDisplays = self.displays.filter(function (d) {
-          return d.configuration === configuration;
-        });
-        (0, _mobx.transaction)(function () {
-          return shownDisplays.forEach(function (d) {
-            return self.displays.remove(d);
-          });
-        });
-        return shownDisplays.length;
-      },
-      replaceDisplay: function replaceDisplay(oldDisplayId, newDisplayId) {
-        var initialSnapshot = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : {};
-        var displayIdx = self.displays.findIndex(function (d) {
-          return d.configuration.displayId === oldDisplayId;
-        });
-
-        if (displayIdx === -1) {
-          throw new Error("could not find display id ".concat(oldDisplayId, " to replace"));
-        }
-
-        var displayTypeConfigSchema = pluginManager.pluggableConfigSchemaType('display');
-        var configuration = (0, _mobxStateTree.resolveIdentifier)(displayTypeConfigSchema, (0, _mobxStateTree.getRoot)(self), newDisplayId);
-        var displayType = pluginManager.getDisplayType(configuration.type);
-
-        if (!displayType) {
-          throw new Error("unknown display type ".concat(configuration.type));
-        }
-
-        self.displays.splice(displayIdx, 1, _objectSpread(_objectSpread({}, initialSnapshot), {}, {
-          type: configuration.type,
-          configuration: configuration
-        }));
-      }
-    };
-  }).views(function (self) {
-    return {
-      trackMenuItems: function trackMenuItems() {
-        var menuItems = [];
-        self.displays.forEach(function (display) {
-          menuItems.push.apply(menuItems, (0, _toConsumableArray2.default)(display.trackMenuItems()));
-        });
-        var displayChoices = [];
-        var view = (0, _util.getContainingView)(self);
-        var viewType = pluginManager.getViewType(view.type);
-        var compatibleDisplayTypes = viewType.displayTypes.map(function (displayType) {
-          return displayType.name;
-        });
-        var compatibleDisplays = self.configuration.displays.filter(function (displayConf) {
-          return compatibleDisplayTypes.includes(displayConf.type);
-        });
-        var shownId = self.displays[0].configuration.displayId;
-
-        if (compatibleDisplays.length > 1) {
-          displayChoices.push({
-            type: 'divider'
-          }, {
-            type: 'subHeader',
-            label: 'Display types'
-          });
-          compatibleDisplays.forEach(function (displayConf) {
-            displayChoices.push({
-              type: 'radio',
-              label: displayConf.type,
-              checked: displayConf.displayId === shownId,
-              onClick: function onClick() {
-                return self.replaceDisplay(shownId, displayConf.displayId);
-              }
+    return mobx_state_tree_1.types
+        .model(trackType, {
+        id: mst_1.ElementId,
+        type: mobx_state_tree_1.types.literal(trackType),
+        configuration: (0, configuration_1.ConfigurationReference)(baseTrackConfig),
+        displays: mobx_state_tree_1.types.array(pluginManager.pluggableMstType('display', 'stateModel')),
+    })
+        .views(self => ({
+        get rpcSessionId() {
+            return self.configuration.trackId;
+        },
+        get name() {
+            return (0, configuration_1.getConf)(self, 'name');
+        },
+        get textSearchAdapter() {
+            return (0, configuration_1.getConf)(self, 'textSearchAdapter');
+        },
+        /**
+         * the PluggableElementType for the currently defined adapter
+         */
+        get adapterType() {
+            const adapterConfig = (0, configuration_1.getConf)(self, 'adapter');
+            const { pluginManager: pm } = (0, mobx_state_tree_1.getEnv)(self);
+            if (!adapterConfig) {
+                throw new Error(`no adapter configuration provided for ${self.type}`);
+            }
+            const adapterType = pm.getAdapterType(adapterConfig.type);
+            if (!adapterType) {
+                throw new Error(`unknown adapter type ${adapterConfig.type}`);
+            }
+            return adapterType;
+        },
+        get viewMenuActions() {
+            const menuItems = [];
+            self.displays.forEach(display => {
+                menuItems.push(...display.viewMenuActions);
+            });
+            return menuItems;
+        },
+        get canConfigure() {
+            const session = (0, util_1.getSession)(self);
+            return ((0, types_1.isSessionModelWithConfigEditing)(session) &&
+                // @ts-ignore
+                (session.adminMode ||
+                    // @ts-ignore
+                    session.sessionTracks.find(track => {
+                        return track.trackId === self.configuration.trackId;
+                    })));
+        },
+    }))
+        .actions(self => ({
+        activateConfigurationUI() {
+            const session = (0, util_1.getSession)(self);
+            const view = (0, util_1.getContainingView)(self);
+            if ((0, types_1.isSessionModelWithConfigEditing)(session)) {
+                // @ts-ignore
+                const trackConf = session.editTrackConfiguration(self.configuration);
+                if (trackConf && trackConf !== self.configuration) {
+                    // @ts-ignore
+                    view.hideTrack(self.configuration);
+                    // @ts-ignore
+                    view.showTrack(trackConf);
+                }
+            }
+        },
+        showDisplay(displayId, initialSnapshot = {}) {
+            const schema = pluginManager.pluggableConfigSchemaType('display');
+            const conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), displayId);
+            const displayType = pluginManager.getDisplayType(conf.type);
+            if (!displayType) {
+                throw new Error(`unknown display type ${conf.type}`);
+            }
+            const display = displayType.stateModel.create({
+                ...initialSnapshot,
+                type: conf.type,
+                configuration: conf,
+            });
+            self.displays.push(display);
+        },
+        hideDisplay(displayId) {
+            const schema = pluginManager.pluggableConfigSchemaType('display');
+            const conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), displayId);
+            const t = self.displays.filter(d => d.conf === conf);
+            (0, mobx_1.transaction)(() => t.forEach(d => self.displays.remove(d)));
+            return t.length;
+        },
+        replaceDisplay(oldId, newId, initialSnapshot = {}) {
+            const idx = self.displays.findIndex(d => d.conf.displayId === oldId);
+            if (idx === -1) {
+                throw new Error(`could not find display id ${oldId} to replace`);
+            }
+            const schema = pluginManager.pluggableConfigSchemaType('display');
+            const conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), newId);
+            const displayType = pluginManager.getDisplayType(conf.type);
+            if (!displayType) {
+                throw new Error(`unknown display type ${conf.type}`);
+            }
+            self.displays.splice(idx, 1, {
+                ...initialSnapshot,
+                type: conf.type,
+                configuration: conf,
             });
-          });
-        }
-
-        return [].concat(menuItems, displayChoices);
-      }
-    };
-  });
-}
+        },
+    }))
+        .views(self => ({
+        trackMenuItems() {
+            const menuItems = [];
+            self.displays.forEach(display => {
+                menuItems.push(...display.trackMenuItems());
+            });
+            const displayChoices = [];
+            const view = (0, util_1.getContainingView)(self);
+            const viewType = pluginManager.getViewType(view.type);
+            const compatibleDisplayTypes = viewType.displayTypes.map(displayType => displayType.name);
+            const compatibleDisplays = self.configuration.displays.filter((displayConf) => compatibleDisplayTypes.includes(displayConf.type));
+            const shownId = self.displays[0].configuration.displayId;
+            if (compatibleDisplays.length > 1) {
+                displayChoices.push({ type: 'divider' }, { type: 'subHeader', label: 'Display types' });
+                compatibleDisplays.forEach((displayConf) => {
+                    displayChoices.push({
+                        type: 'radio',
+                        label: displayConf.type,
+                        checked: displayConf.displayId === shownId,
+                        onClick: () => self.replaceDisplay(shownId, displayConf.displayId),
+                    });
+                });
+            }
+            return [...menuItems, ...displayChoices];
+        },
+    }));
+}
+exports.createBaseTrackModel = createBaseTrackModel;

package/pluggableElementTypes/models/BaseViewModel.js

@@ -1,42 +1,26 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _mst = require("../../util/types/mst");
-
-var BaseViewModel = _mobxStateTree.types.model('BaseView', {
-  id: _mst.ElementId,
-  displayName: _mobxStateTree.types.maybe(_mobxStateTree.types.string)
-}).volatile(function
-  /* self */
-() {
-  return {
-    width: 800
-  };
-}).views(function
-  /* self */
-() {
-  return {
-    menuItems: function menuItems() {
-      return [];
-    }
-  };
-}).actions(function (self) {
-  return {
-    setDisplayName: function setDisplayName(name) {
-      self.displayName = name;
+Object.defineProperty(exports, "__esModule", { value: true });
+const mobx_state_tree_1 = require("mobx-state-tree");
+const mst_1 = require("../../util/types/mst");
+const BaseViewModel = mobx_state_tree_1.types
+    .model('BaseView', {
+    id: mst_1.ElementId,
+    displayName: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
+})
+    .volatile(( /* self */) => ({
+    width: 800,
+}))
+    .views(( /* self */) => ({
+    menuItems() {
+        return [];
     },
-    setWidth: function setWidth(newWidth) {
-      self.width = newWidth;
-    }
-  };
-});
-
-var _default = BaseViewModel; // eslint-disable-next-line @typescript-eslint/no-empty-interface
-
-exports.default = _default;
+}))
+    .actions(self => ({
+    setDisplayName(name) {
+        self.displayName = name;
+    },
+    setWidth(newWidth) {
+        self.width = newWidth;
+    },
+}));
+exports.default = BaseViewModel;