@jbrowse/plugin-data-management 1.7.10 → 1.7.11

package/dist/HierarchicalTrackSelectorWidget/components/CloseConnectionDialog.d.ts

@@ -1,6 +1,12 @@
 /// <reference types="react" />
 declare function CloseConnectionDialog({ modalInfo, setModalInfo, }: {
-    modalInfo: any;
+    modalInfo?: {
+        name?: string;
+        dereferenceTypeCount?: {
+            [key: string]: number;
+        };
+        safelyBreakConnection?: Function;
+    };
     setModalInfo: Function;
 }): JSX.Element;
 declare const _default: typeof CloseConnectionDialog;

package/dist/HierarchicalTrackSelectorWidget/components/CloseConnectionDialog.js

@@ -34,16 +34,13 @@ function CloseConnectionDialog(_ref) {
     }, "".concat(value, " ").concat(key));
   }))) : null, /*#__PURE__*/_react.default.createElement(_core.DialogContentText, null, "Are you sure you want to close this connection?")), /*#__PURE__*/_react.default.createElement(_core.DialogActions, null, /*#__PURE__*/_react.default.createElement(_core.Button, {
     onClick: function onClick() {
-      setModalInfo();
+      return setModalInfo();
     },
     color: "primary"
   }, "Cancel"), /*#__PURE__*/_react.default.createElement(_core.Button, {
     variant: "contained",
     onClick: modalInfo ? function () {
-      if (safelyBreakConnection) {
-        safelyBreakConnection();
-      }
-
+      safelyBreakConnection === null || safelyBreakConnection === void 0 ? void 0 : safelyBreakConnection();
       setModalInfo();
     } : function () {},
     color: "primary"

package/dist/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.d.ts

@@ -7,7 +7,7 @@ declare function DeleteConnectionDialog({ deleteDialogDetails, session, handleCl
         connectionConf: AnyConfigurationModel;
     };
     session: AbstractSessionModel;
-    handleClose: Function;
+    handleClose: () => void;
 }): JSX.Element;
 declare const _default: typeof DeleteConnectionDialog;
 export default _default;

package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.d.ts

@@ -1,6 +1,10 @@
+import { HierarchicalTrackSelectorModel } from '../model';
+declare const HierarchicalTrackSelectorContainer: ({ model, toolbarHeight, overrideDimensions, }: {
+    model: HierarchicalTrackSelectorModel;
+    toolbarHeight: number;
+    overrideDimensions?: {
+        width: number;
+        height: number;
+    } | undefined;
+}) => JSX.Element;
 export default HierarchicalTrackSelectorContainer;
-declare function HierarchicalTrackSelectorContainer({ model, toolbarHeight, overrideDimensions }: {
-    model: any;
-    toolbarHeight: any;
-    overrideDimensions: any;
-}): JSX.Element;

package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js

@@ -53,6 +53,7 @@ function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "functio
 
 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; }
 
+// lazy components
 var CloseConnectionDialog = /*#__PURE__*/(0, _react.lazy)(function () {
   return Promise.resolve().then(function () {
     return _interopRequireWildcard(require('./CloseConnectionDialog'));
@@ -127,10 +128,11 @@ var useStyles = (0, _core.makeStyles)(function (theme) {
       margin: 'auto 0'
     }
   };
-}); // An individual node in the track selector. Note: manually sets cursor:
-// pointer improves usability for what can be clicked
+});
 
-var Node = function Node(props) {
+// An individual node in the track selector. Note: manually sets cursor:
+// pointer improves usability for what can be clicked
+function Node(props) {
   var data = props.data,
       isOpen = props.isOpen,
       style = props.style,
@@ -148,7 +150,7 @@ var Node = function Node(props) {
   var classes = useStyles();
   var width = 10;
   var marginLeft = nestingLevel * width + (isLeaf ? width : 0);
-  var unsupported = name && (name.endsWith('(Unsupported)') || name.endsWith('(Unknown)'));
+  var unsupported = (name === null || name === void 0 ? void 0 : name.endsWith('(Unsupported)')) || (name === null || name === void 0 ? void 0 : name.endsWith('(Unknown)'));
   var description = conf && (0, _configuration.readConfObject)(conf, ['description']) || '';
   return /*#__PURE__*/_react.default.createElement("div", {
     style: style,
@@ -158,7 +160,7 @@ var Node = function Node(props) {
       key: "mark-".concat(idx),
       style: {
         left: idx * width + 4,
-        height: style.height
+        height: style === null || style === void 0 ? void 0 : style.height
       },
       className: classes.nestingLevelMarker
     });
@@ -191,6 +193,7 @@ var Node = function Node(props) {
       color: "primary",
       disabled: unsupported,
       inputProps: {
+        // @ts-ignore
         'data-testid': "htsTrackEntry-".concat(id)
       }
     }),
@@ -206,9 +209,9 @@ var Node = function Node(props) {
     color: "secondary",
     "data-testid": "htsTrackEntryMenu-".concat(id)
   }, /*#__PURE__*/_react.default.createElement(_MoreHoriz.default, null))))));
-};
+}
 
-var getNodeData = function getNodeData(node, nestingLevel, extra) {
+function getNodeData(node, nestingLevel, extra) {
   var isLeaf = !!node.conf;
   return {
     data: _objectSpread(_objectSpread({
@@ -220,11 +223,11 @@ var getNodeData = function getNodeData(node, nestingLevel, extra) {
     nestingLevel: nestingLevel,
     node: node
   };
-}; // this is the main tree component for the hierarchical track selector in note:
+}
+
+// this is the main tree component for the hierarchical track selector in note:
 // in jbrowse-web the toolbar is position="sticky" which means the autosizer
 // includes the height of the toolbar, so we subtract the given offsets
-
-
 var HierarchicalTree = (0, _mobxReact.observer)(function (_ref) {
   var _session$getTrackActi;
 
@@ -255,7 +258,7 @@ var HierarchicalTree = (0, _mobxReact.observer)(function (_ref) {
     };
   }, [view, model, drawerPosition]);
   var treeWalker = (0, _react.useCallback)( /*#__PURE__*/_regenerator.default.mark(function treeWalker() {
-    var i, parentMeta, _i, curr;
+    var i, r, parentMeta, _i, curr;
 
     return _regenerator.default.wrap(function treeWalker$(_context) {
       while (1) {
@@ -265,51 +268,52 @@ var HierarchicalTree = (0, _mobxReact.observer)(function (_ref) {
 
           case 1:
             if (!(i < tree.children.length)) {
-              _context.next = 7;
+              _context.next = 8;
               break;
             }
 
-            _context.next = 4;
-            return getNodeData(tree.children[i], 0, extra);
+            r = tree.children[i];
+            _context.next = 5;
+            return getNodeData(r, 0, extra);
 
-          case 4:
+          case 5:
             i++;
             _context.next = 1;
             break;
 
-          case 7:
+          case 8:
             if (!true) {
-              _context.next = 21;
+              _context.next = 22;
               break;
             }
 
-            _context.next = 10;
+            _context.next = 11;
             return;
 
-          case 10:
+          case 11:
             parentMeta = _context.sent;
             _i = 0;
 
-          case 12:
+          case 13:
             if (!(_i < parentMeta.node.children.length)) {
-              _context.next = 19;
+              _context.next = 20;
               break;
             }
 
             curr = parentMeta.node.children[_i];
-            _context.next = 16;
+            _context.next = 17;
             return getNodeData(curr, parentMeta.nestingLevel + 1, extra);
 
-          case 16:
+          case 17:
             _i++;
-            _context.next = 12;
+            _context.next = 13;
             break;
 
-          case 19:
-            _context.next = 7;
+          case 20:
+            _context.next = 8;
             break;
 
-          case 21:
+          case 22:
           case "end":
             return _context.stop();
         }
@@ -319,6 +323,7 @@ var HierarchicalTree = (0, _mobxReact.observer)(function (_ref) {
   var conf = info === null || info === void 0 ? void 0 : info.conf;
   var menuItems = conf && ((_session$getTrackActi = session.getTrackActionMenuItems) === null || _session$getTrackActi === void 0 ? void 0 : _session$getTrackActi.call(session, conf)) || [];
   (0, _react.useEffect)(function () {
+    // @ts-ignore
     treeRef.current.recomputeTree({
       refreshNodes: true,
       useDefaultHeight: true
@@ -387,17 +392,18 @@ var HierarchicalTrackSelectorContainer = (0, _mobxReact.observer)(function (_ref
     setAnchorEl(null);
   }
 
+  var hasConnections = (0, _util.isSessionModelWithConnections)(session);
+  var hasAddTrack = (0, _util.isSessionWithAddTracks)(session);
   return /*#__PURE__*/_react.default.createElement(Wrapper, {
     overrideDimensions: overrideDimensions
   }, /*#__PURE__*/_react.default.createElement(HierarchicalTrackSelector, {
     model: model,
-    toolbarHeight: toolbarHeight,
-    overrideDimensions: overrideDimensions
-  }), session.addConnectionConf || session.addTrackConf ? /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, /*#__PURE__*/_react.default.createElement(_core.Fab, {
+    toolbarHeight: toolbarHeight
+  }), hasAddTrack || hasConnections ? /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, /*#__PURE__*/_react.default.createElement(_core.Fab, {
     color: "secondary",
     className: classes.fab,
     onClick: function onClick(event) {
-      setAnchorEl(event.currentTarget);
+      return setAnchorEl(event.currentTarget);
     }
   }, /*#__PURE__*/_react.default.createElement(_Add.default, null)), /*#__PURE__*/_react.default.createElement(_core.Menu, {
     anchorEl: anchorEl,
@@ -405,19 +411,23 @@ var HierarchicalTrackSelectorContainer = (0, _mobxReact.observer)(function (_ref
     onClose: function onClose() {
       return setAnchorEl(null);
     }
-  }, session.addConnectionConf ? /*#__PURE__*/_react.default.createElement(_core.MenuItem, {
+  }, hasConnections ? /*#__PURE__*/_react.default.createElement(_core.MenuItem, {
     onClick: function onClick() {
       handleFabClose();
-      var widget = session.addWidget('AddConnectionWidget', 'addConnectionWidget');
-      session.showWidget(widget);
+
+      if ((0, _util.isSessionModelWithWidgets)(session)) {
+        session.showWidget(session.addWidget('AddConnectionWidget', 'addConnectionWidget'));
+      }
     }
-  }, "Add connection") : null, session.addTrackConf ? /*#__PURE__*/_react.default.createElement(_core.MenuItem, {
+  }, "Add connection") : null, hasAddTrack ? /*#__PURE__*/_react.default.createElement(_core.MenuItem, {
     onClick: function onClick() {
       handleFabClose();
-      var widget = session.addWidget('AddTrackWidget', 'addTrackWidget', {
-        view: model.view.id
-      });
-      session.showWidget(widget);
+
+      if ((0, _util.isSessionModelWithWidgets)(session)) {
+        session.showWidget(session.addWidget('AddTrackWidget', 'addTrackWidget', {
+          view: model.view.id
+        }));
+      }
     }
   }, "Add track") : null)) : null);
 });
@@ -463,7 +473,8 @@ var HierarchicalTrackSelectorHeader = (0, _mobxReact.observer)(function (_ref6)
   var assemblyName = assemblyNames[assemblyIdx];
 
   function breakConnection(connectionConf, deletingConnection) {
-    var name = (0, _configuration.readConfObject)(connectionConf, 'name');
+    var name = (0, _configuration.readConfObject)(connectionConf, 'name'); // @ts-ignore
+
     var result = session.prepareToBreakConnection(connectionConf);
 
     if (result) {
@@ -498,11 +509,14 @@ var HierarchicalTrackSelectorHeader = (0, _mobxReact.observer)(function (_ref6)
     }
   }];
 
-  if (session.addConnectionConf) {
+  if ((0, _util.isSessionModelWithConnections)(session)) {
     connectionMenuItems.unshift({
       label: 'Add connection',
       onClick: function onClick() {
-        session.showWidget(session.addWidget('AddConnectionWidget', 'addConnectionWidget'));
+        if ((0, _util.isSessionModelWithWidgets)(session)) {
+          var widget = session.addWidget('AddConnectionWidget', 'addConnectionWidget');
+          session.showWidget(widget);
+        }
       }
     });
     connectionMenuItems.push({
@@ -519,7 +533,7 @@ var HierarchicalTrackSelectorHeader = (0, _mobxReact.observer)(function (_ref6)
       return {
         label: name,
         onClick: function onClick() {
-          setAssemblyIdx(idx);
+          return setAssemblyIdx(idx);
         }
       };
     })
@@ -527,9 +541,12 @@ var HierarchicalTrackSelectorHeader = (0, _mobxReact.observer)(function (_ref6)
   var menuItems = [{
     label: 'Add track...',
     onClick: function onClick() {
-      session.showWidget(session.addWidget('AddTrackWidget', 'addTrackWidget', {
-        view: model.view.id
-      }));
+      if ((0, _util.isSessionModelWithWidgets)(session)) {
+        var widget = session.addWidget('AddTrackWidget', 'addTrackWidget', {
+          view: model.view.id
+        });
+        session.showWidget(widget);
+      }
     }
   }].concat(assemblyMenuItems);
   return /*#__PURE__*/_react.default.createElement("div", {
@@ -541,15 +558,15 @@ var HierarchicalTrackSelectorHeader = (0, _mobxReact.observer)(function (_ref6)
     style: {
       display: 'flex'
     }
-  }, session.addTrackConf && /*#__PURE__*/_react.default.createElement(_core.IconButton, {
+  }, (0, _util.isSessionWithAddTracks)(session) && /*#__PURE__*/_react.default.createElement(_core.IconButton, {
     className: classes.menuIcon,
     onClick: function onClick(event) {
-      setMenuAnchorEl(event.currentTarget);
+      return setMenuAnchorEl(event.currentTarget);
     }
   }, /*#__PURE__*/_react.default.createElement(_Menu.default, null)), session.makeConnection && /*#__PURE__*/_react.default.createElement(_core.IconButton, {
     className: classes.menuIcon,
     onClick: function onClick(event) {
-      setConnectionAnchorEl(event.currentTarget);
+      return setConnectionAnchorEl(event.currentTarget);
     }
   }, /*#__PURE__*/_react.default.createElement(_Icons.Cable, null)), /*#__PURE__*/_react.default.createElement(_core.TextField, {
     className: classes.searchBox,
@@ -593,8 +610,7 @@ var HierarchicalTrackSelectorHeader = (0, _mobxReact.observer)(function (_ref6)
     fallback: /*#__PURE__*/_react.default.createElement("div", null)
   }, modalInfo ? /*#__PURE__*/_react.default.createElement(CloseConnectionDialog, {
     modalInfo: modalInfo,
-    setModalInfo: setModalInfo,
-    session: session
+    setModalInfo: setModalInfo
   }) : deleteDialogDetails ? /*#__PURE__*/_react.default.createElement(DeleteConnectionDialog, {
     handleClose: function handleClose() {
       return setDeleteDialogDetails(undefined);

package/dist/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.d.ts

@@ -1,9 +1,10 @@
 /// <reference types="react" />
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { AbstractSessionModel } from '@jbrowse/core/util';
 declare function ManageConnectionsDlg({ session, handleClose, breakConnection, }: {
     handleClose: () => void;
     session: AbstractSessionModel;
-    breakConnection: Function;
+    breakConnection: (conf: AnyConfigurationModel, arg: boolean) => void;
 }): JSX.Element;
 declare const _default: typeof ManageConnectionsDlg;
 export default _default;

package/dist/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.d.ts

@@ -1,10 +1,11 @@
 /// <reference types="react" />
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { AbstractSessionModel } from '@jbrowse/core/util';
 declare function ToggleConnectionDialog({ session, handleClose, assemblyName, breakConnection, }: {
     handleClose: () => void;
     session: AbstractSessionModel;
     assemblyName: string;
-    breakConnection: Function;
+    breakConnection: (arg: AnyConfigurationModel) => void;
 }): JSX.Element;
 declare const _default: typeof ToggleConnectionDialog;
 export default _default;

package/dist/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js

@@ -39,7 +39,8 @@ function ToggleConnectionDialog(_ref) {
       breakConnection = _ref.breakConnection;
   var classes = useStyles();
   var connections = session.connections,
-      connectionInstances = session.connectionInstances;
+      _session$connectionIn = session.connectionInstances,
+      instances = _session$connectionIn === void 0 ? [] : _session$connectionIn;
   var assemblySpecificConnections = connections.filter(function (c) {
     var configAssemblyNames = (0, _configuration.readConfObject)(c, 'assemblyNames');
 
@@ -62,17 +63,15 @@ function ToggleConnectionDialog(_ref) {
     className: classes.connectionContainer
   }, assemblySpecificConnections.map(function (conf) {
     var name = (0, _configuration.readConfObject)(conf, 'name');
-    return /*#__PURE__*/_react.default.createElement("div", {
-      key: conf.connectionId
-    }, /*#__PURE__*/_react.default.createElement(_core.FormControlLabel, {
+    var found = instances.find(function (conn) {
+      return name === conn.name;
+    });
+    return /*#__PURE__*/_react.default.createElement(_core.FormControlLabel, {
+      key: conf.connectionId,
       control: /*#__PURE__*/_react.default.createElement(_core.Checkbox, {
-        checked: !!(connectionInstances !== null && connectionInstances !== void 0 && connectionInstances.find(function (conn) {
-          return name === conn.name;
-        })),
+        checked: !!found,
         onChange: function onChange() {
-          if (connectionInstances !== null && connectionInstances !== void 0 && connectionInstances.find(function (conn) {
-            return conn.name === (0, _configuration.readConfObject)(conf, 'name');
-          })) {
+          if (found) {
             breakConnection(conf);
           } else {
             var _session$makeConnecti;
@@ -83,7 +82,7 @@ function ToggleConnectionDialog(_ref) {
         color: "primary"
       }),
       label: name
-    }));
+    });
   }), !assemblySpecificConnections.length ? /*#__PURE__*/_react.default.createElement(_core.Typography, null, "No connections found for ", assemblyName) : null)), /*#__PURE__*/_react.default.createElement(_core.DialogActions, null, /*#__PURE__*/_react.default.createElement(_core.Button, {
     onClick: function onClick() {
       return handleClose();

package/dist/HierarchicalTrackSelectorWidget/index.d.ts

@@ -1,2 +1,2 @@
-export { default as stateModelFactory } from "./model";
-export const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export { default as stateModelFactory } from './model';
+export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/dist/HierarchicalTrackSelectorWidget/model.d.ts

@@ -1,37 +1,59 @@
-export function generateHierarchy(model: any, trackConfigurations: any, collapsed: any): never[];
-declare function _default(pluginManager: any): import("mobx-state-tree").IModelType<{
+import { Instance } from 'mobx-state-tree';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { AbstractView } from 'react';
+export declare type TreeNode = {
+    name: string;
+    id: string;
+    conf?: AnyConfigurationModel;
+    checked?: boolean;
+    isOpenByDefault?: boolean;
+    children: TreeNode[];
+};
+export declare function generateHierarchy(model: HierarchicalTrackSelectorModel, trackConfigurations: AnyConfigurationModel[], collapsed: {
+    get: (arg: string) => boolean | undefined;
+}): TreeNode[];
+export default function stateTreeFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"HierarchicalTrackSelectorWidget">;
     collapsed: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
     filterText: import("mobx-state-tree").IType<string | undefined, string, string>;
-    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<any>>;
+    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
 }, {
-    setView(view: any): void;
-    toggleCategory(pathName: any): void;
+    setView(view: AbstractView): void;
+    toggleCategory(pathName: string): void;
     clearFilterText(): void;
-    setFilterText(newText: any): void;
+    setFilterText(newText: string): void;
 } & {
-    getRefSeqTrackConf(assemblyName: any): any;
-    trackConfigurations(assemblyName: any): any[];
-    readonly assemblyNames: any;
-    connectionTrackConfigurations(assemblyName: any, connection: any): any;
-    hierarchy(assemblyName: any): {
+    getRefSeqTrackConf(assemblyName: string): any;
+} & {
+    trackConfigurations(assemblyName: string): any[];
+    readonly assemblyNames: string[];
+    connectionTrackConfigurations(assemblyName: string, connection: {
+        tracks: AnyConfigurationModel[];
+    }): (import("mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+} & {
+    hierarchy(assemblyName: string): {
         name: string;
         id: string;
         children: ({
             id: any;
             name: any;
-            children: never[];
+            children: TreeNode[];
             state: {
                 expanded: boolean;
             };
         } | {
             name: string;
             id: string;
-            children: any[];
+            children: TreeNode[];
         })[];
     };
-    connectionHierarchy(assemblyName: any, connection: any): never[];
-    allTracksInCategoryPath(path: any, connection: any, assemblyName: any): {};
+    connectionHierarchy(assemblyName: string, connection: {
+        tracks: AnyConfigurationModel[];
+    }): TreeNode[];
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export default _default;
+export declare type HierarchicalTrackSelectorStateModel = ReturnType<typeof stateTreeFactory>;
+export declare type HierarchicalTrackSelectorModel = Instance<HierarchicalTrackSelectorStateModel>;